R3KK66 last accessed: 2022-11-04

rcsb_pdb
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:27.464785

Other names: RCSB PDB, rcsb_pdb

This resource is powered by the Protein Data Bank archive-information about the 3D shapes of proteins, nucleic acids, and complex assemblies that helps students and researchers understand all aspects of biomedicine and agriculture, from protein synthesis to health and disease. As a member of the wwPDB, the RCSB PDB curates and annotates PDB data. The RCSB PDB builds upon the data by creating tools and resources for research and education in molecular biology, structural biology, computational biology, and beyond.

Webpage:

http://rcsb.org

Licence:

Name: Open Data Commons (ODC) Public Domain Dedication and Licence (PDDL) 1.0
URL: http://opendatacommons.org/licenses/pddl/1.0/

Publications:

Publications
More detailed information about this field from each metasource.

The Protein Data Bank
PMID: 10592235
metasource: Fairsharing.org
version: FAIRsharing.org: RCSB PDB; RCSB Protein Data Bank; DOI: https://doi.org/10.25504/FAIRsharing.2t35ja; Last edited: April 26, 2021, 2:57 p.m.; Last accessed: Jan 03 2022 7:05 p.m.

RCSB Protein Data Bank: Improved Annotation, Search, and Visualization of Membrane Protein Structures Archived in the PDB
PMID: 34864908
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:27.464785

https://doi.org/10.1093/nar/gkaa1038
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

The Protein Data Bank PubMed citations: 9999.

9999 articles citing: The Protein Data Bank

Isolation and characterization of phage display-derived scFv antibodies against human parechovirus 1 VP0 protein. PMID:35927325
On-the-fly investigation of XUV excited large molecular ions using a high harmonic generation light source. PMID:35915132
LARGE-SCALE MULTIPLE INFERENCE OF COLLECTIVE DEPENDENCE WITH APPLICATIONS TO PROTEIN FUNCTION. PMID:35910493
Newly Synthesized Pyrazolinone Chalcones as Anticancer Agents via Inhibiting the PI3K/Akt/ERK1/2 Signaling Pathway. PMID:35910116
Structural determinants of DNA recognition by the NO sensor NsrR and related Rrf2-type [FeS]-transcription factors. PMID:35908109
Multi-Omics Interdisciplinary Research Integration to Accelerate Dementia Biomarker Development (MIRIADE). PMID:35903119
Hydrophilic But Not Hydrophobic Surfactant Protein Genetic Variants Are Associated With Severe Acute Respiratory Syncytial Virus Infection in Children. PMID:35903101
Uniform binding and negative catalysis at the origin of enzymes. PMID:35900021
Network Pharmacology and Molecular Docking on the Molecular Mechanism of Jiawei-Huang Lian-Gan Jiang Decoction in the Treatment of Colorectal Adenomas. PMID:35899228
Harnessing Protein-Ligand Interaction Fingerprints to Predict New Scaffolds of RIPK1 Inhibitors. PMID:35897894
A Cheminformatics Study Regarding the Human Health Risks Assessment of the Stereoisomers of Difenoconazole. PMID:35897858
Combining empirical knowledge, in silico molecular docking and ADMET profiling to identify therapeutic phytochemicals from Brucea antidysentrica for acute myeloid leukemia. PMID:35895695
The Local Topological Free Energy of the SARS-CoV-2 Spike Protein. PMID:35893978
Exploring the Binding Interaction of Active Compound of Pineapple against Foodborne Bacteria and Novel Coronavirus (SARS-CoV-2) Based on Molecular Docking and Simulation Studies. PMID:35893899
Cross-Species Analysis of Innate Immune Antagonism by Cytomegalovirus IE1 Protein. PMID:35893691
Galectin-9 and Interferon-Gamma Are Released by Natural Killer Cells upon Activation with Interferon-Alpha and Orchestrate the Suppression of Hepatitis C Virus Infection. PMID:35891518
Potential Autoimmunity Resulting from Molecular Mimicry between SARS-CoV-2 Spike and Human Proteins. PMID:35891400
Novel Cyclic Peptides for Targeting EGFR and EGRvIII Mutation for Drug Delivery. PMID:35890400
A Study on the Anti-NF-κB, Anti-Candida, and Antioxidant Activities of Two Natural Plant Hormones: Gibberellin A4 and A7. PMID:35890244
Palladium(II) Complexes of Substituted Salicylaldehydes: Synthesis, Characterization and Investigation of Their Biological Profile. PMID:35890184
Synthesis of Functionalized N-(4-Bromophenyl)furan-2-carboxamides via Suzuki-Miyaura Cross-Coupling: Anti-Bacterial Activities against Clinically Isolated Drug Resistant A. baumannii, K. pneumoniae, E. cloacae and MRSA and Its Validation via a Computational Approach. PMID:35890140
Protein-Ligand Docking in the Machine-Learning Era. PMID:35889440
Molecular Docking and Dynamics Simulation of Natural Compounds from Betel Leaves (Piper betle L.) for Investigating the Potential Inhibition of Alpha-Amylase and Alpha-Glucosidase of Type 2 Diabetes. PMID:35889399
Allostery Inhibition of BACE1 by Psychotic and Meroterpenoid Drugs in Alzheimer's Disease Therapy. PMID:35889246
Membrane Permeabilization and Antimicrobial Activity of Recombinant Defensin-d2 and Actifensin against Multidrug-Resistant Pseudomonas aeruginosa and Candida albicans. PMID:35889198
SARS-CoV-2 Amino Acid Mutations Detection in Greek Patients Infected in the First Wave of the Pandemic. PMID:35889149
Comparative Analysis of Catabolic and Anabolic Dehydroshikimate Dehydratases for 3,4-DHBA Production in Escherichia coli. PMID:35889076
Survey of the Intermolecular Disulfide Bonds Observed in Protein Crystal Structures Deposited in the Protein Data Bank. PMID:35888076
Discovery of Small Molecules from Echinacea angustifolia Targeting RNA-Dependent RNA Polymerase of Japanese Encephalitis Virus. PMID:35888042
Ligand-Enhanced Negative Images Optimized for Docking Rescoring. PMID:35887220
Connexins and Pannexins-Similarities and Differences According to the FOD-M Model. PMID:35884807
Valeriana pilosa Roots Essential Oil: Chemical Composition, Antioxidant Activities, and Molecular Docking Studies on Enzymes Involved in Redox Biological Processes. PMID:35883828
Benchmarking the Accuracy of AlphaFold 2 in Loop Structure Prediction. PMID:35883541
Exploring TRPC3 Interaction with Cholesterol through Coarse-Grained Molecular Dynamics Simulations. PMID:35883446
l-Ornithine-N5-monooxygenase (PvdA) Substrate Analogue Inhibitors for Pseudomonas aeruginosa Infections Treatment: Drug Repurposing Computational Studies. PMID:35883443
Tertiary and Quaternary Structure Organization in GMP Synthetases: Implications for Catalysis. PMID:35883427
What Makes GPCRs from Different Families Bind to the Same Ligand? PMID:35883418
Integrated structure-based protein interface prediction. PMID:35879651
DES-Amyloidoses "Amyloidoses through the looking-glass": A knowledgebase developed for exploring and linking information related to human amyloid-related diseases. PMID:35877764
Combined Theoretical and Experimental Study to Unravel the Differences in Promiscuous Amidase Activity of Two Nonhomologous Enzymes. PMID:35875595
Computational methods and theory for ion channel research. PMID:35874965
Implementing a Scoring Function Based on Interaction Fingerprint for Autogrow4: Protein Kinase CK1δ as a Case Study. PMID:35874609
Assessing the clinical utility of protein structural analysis in genomic variant classification: experiences from a diagnostic laboratory. PMID:35869530
Machine intelligence-driven framework for optimized hit selection in virtual screening. PMID:35869511
Structure-based prediction of BRAF mutation classes using machine-learning approaches. PMID:35869122
Molecular docking analysis and evaluation of the antimicrobial properties of the constituents of Geranium wallichianum D. Don ex Sweet from Kashmir Himalaya. PMID:35869098
In silico toxicology: From structure-activity relationships towards deep learning and adverse outcome pathways. PMID:35866138
Taohong Siwu Decoction exerts anticancer effects on breast cancer via regulating MYC, BIRC5, EGF and PIK3R1 revealed by HTS2 technology. PMID:35860405
Probing Watson-Crick and Hoogsteen base pairing in duplex DNA using dynamic nuclear polarization solid-state NMR spectroscopy. PMID:35857870
The two-domain elevator-type mechanism of zinc-transporting ZIP proteins. PMID:35857505
Selective activation of Gαob by an adenosine A1 receptor agonist elicits analgesia without cardiorespiratory depression. PMID:35851064
Sodium and Magnesium Ion Location at the Backbone and at the Nucleobase of RNA: Ab Initio Molecular Dynamics in Water Solution. PMID:35847262
A Path-Based Analysis of Infected Cell Line and COVID-19 Patient Transcriptome Reveals Novel Potential Targets and Drugs Against SARS-CoV-2. PMID:35844595
A Structure-Based B-cell Epitope Prediction Model Through Combing Local and Global Features. PMID:35844532
Allosteric Hotspots in the Main Protease of SARS-CoV-2. PMID:35843284
Deep learning frameworks for protein-protein interaction prediction. PMID:35832624
A comparative analysis of machine learning classifiers for predicting protein-binding nucleotides in RNA sequences. PMID:35832617
Mode of action of fluopyram in plant-parasitic nematodes. PMID:35831379
Model building of protein complexes from intermediate-resolution cryo-EM maps with deep learning-guided automatic assembly. PMID:35831370
De-etiolation-induced protein 1 (DEIP1) mediates assembly of the cytochrome b6f complex in Arabidopsis. PMID:35831297
Artificial intelligence and machine-learning approaches in structure and ligand-based discovery of drugs affecting central nervous system. PMID:35819579
Towards Covid-19 TMPRSS2 enzyme inhibitors and antimicrobial agents: Synthesis, antimicrobial potency, molecular docking, and drug-likeness prediction of thiadiazole-triazole hybrids. PMID:35818577
Progressive membrane-binding mechanism of SARS-CoV-2 variant spike proteins. PMID:35813872
De novo metalloprotein design. PMID:35811759
Molecular docking and machine learning affinity prediction of compounds identified upon softwood bark extraction to the main protease of the SARS-CoV-2 virus. PMID:35810518
Phylodynamics and Coat Protein Analysis of Babaco Mosaic Virus in Ecuador. PMID:35807598
Disentangling Unusual Catalytic Properties and the Role of the [4Fe-4S] Cluster of Three Endonuclease III from the Extremophile D. radiodurans. PMID:35807515
Decoding the Effect of Hydrostatic Pressure on TRPV1 Lower-Gate Conformation by Molecular-Dynamics Simulation. PMID:35806371
Investigation of Structural Features of Two Related Lipases and the Impact on Fatty Acid Specificity in Vegetable Fats. PMID:35806072
Protein-Protein Interaction Prediction for Targeted Protein Degradation. PMID:35806036
RPpocket: An RNA-Protein Intuitive Database with RNA Pocket Topology Resources. PMID:35805909
Exploration of Somatostatin Binding Mechanism to Somatostatin Receptor Subtype 4. PMID:35805885
Comparative bioinformatics analysis and abiotic stress responses of expansin proteins in Cucurbitaceae members: watermelon and melon. PMID:35804193
Peptidomimetic inhibitors of TMPRSS2 block SARS-CoV-2 infection in cell culture. PMID:35804152
Pycard and BC017158 Candidate Genes of Irm1 Locus Modulate Inflammasome Activation for IL-1β Production. PMID:35799794
Comparative Analysis on Alignment-Based and Pretrained Feature Representations for the Identification of DNA-Binding Proteins. PMID:35799660
Insights into the xylan degradation system of Cellulomonas sp. B6: biochemical characterization of rCsXyn10A and rCsAbf62A. PMID:35799069
A structural homology approach to identify potential cross-reactive antibody responses following SARS-CoV-2 infection. PMID:35794133
The Elephant Evolved p53 Isoforms that Escape MDM2-Mediated Repression and Cancer. PMID:35792674
Serial crystallography with multi-stage merging of thousands of images. PMID:35787556
Protective Effect of Hedyotis diffusa Willd. Ethanol Extract on Isoniazid-Induced Liver Injury in the Zebrafish Model. PMID:35783199
An alanine to valine mutation of glutamyl-tRNA reductase enhances 5-aminolevulinic acid synthesis in rice. PMID:35779128
Fully Flexible Ligand Docking for the P2X7 Receptor Using ROSIE. PMID:35776320
Sequence-assignment validation in cryo-EM models with checkMySequence. PMID:35775980
Linear Epitope Binding Patterns of Grass Pollen-Specific Antibodies in Allergy and in Response to Allergen-Specific Immunotherapy. PMID:35769580
Rapid prediction of protein natural frequencies using graph neural networks. PMID:35769204
FGDB: a comprehensive graph database of ligand fragments from the Protein Data Bank. PMID:35763362
What the protein data bank tells us about the evolutionary conservation of protein conformational diversity. PMID:35762711
Characterization of a new L-carnosine synthase mined from deep-sea sediment metagenome. PMID:35761267
Insights from a computational analysis of the SARS-CoV-2 Omicron variant: Host-pathogen interaction, pathogenicity, and possible drug therapeutics. PMID:35759231
SLC7A11/GPX4 Inactivation-Mediated Ferroptosis Contributes to the Pathogenesis of Triptolide-Induced Cardiotoxicity. PMID:35757509
An Overview of Alphafold's Breakthrough. PMID:35757294
Prediction of infectivity of SARS-CoV2: Mathematical model with analysis of docking simulation for spike proteins and angiotensin-converting enzyme 2. PMID:35756961
Accurate modeling of RNA hairpins through the explicit treatment of electronic polarizability with the classical Drude oscillator force field. PMID:35756549
Entropies Derived from the Packing Geometries within a Single Protein Structure. PMID:35755337
3pHLA-score improves structure-based peptide-HLA binding affinity prediction. PMID:35750701
Coarse-grained modeling of the calcium, sodium, magnesium and potassium cations interacting with proteins. PMID:35748949
A New Variant of Mutational and Polymorphic Signatures in the ERG11 Gene of Fluconazole-Resistant Candida albicans. PMID:35747333
Borneol Ester Derivatives as Entry Inhibitors of a Wide Spectrum of SARS-CoV-2 Viruses. PMID:35746766
Irreversible Antagonists for the Adenosine A2B Receptor. PMID:35744918
TCGA-My: A Systematic Repository for Systems Biology of Malaysian Colorectal Cancer. PMID:35743803
Genome-Wide Identification of m6A Writers, Erasers and Readers in Poplar 84K. PMID:35741780
A Quantitative Proteomic Approach Explores the Possible Mechanisms by Which the Small Molecule Stemazole Promotes the Survival of Human Neural Stem Cells. PMID:35741576
Network pharmacology integrated molecular dynamics reveals the bioactive compounds and potential targets of Tinospora crispa Linn. as insulin sensitizer. PMID:35737707
Computer-Aided Analysis of West Sub-Saharan Africa Snakes Venom towards the Design of Epitope-Based Poly-Specific Antivenoms. PMID:35737079
UHPLC-MS Metabolomic Fingerprinting, Antioxidant, and Enzyme Inhibition Activities of Himantormia lugubris from Antarctica. PMID:35736493
Prediction of Angiopoietin-like Protein 4-related Signaling Pathways in Cholangiocarcinoma Cells. PMID:35732325
Withania somnifera phytochemicals possess SARS-CoV-2 RdRp and human TMPRSS2 protein binding potential. PMID:35729946
Multi-task learning to leverage partially annotated data for PPI interface prediction. PMID:35729253
Molecular Structure-Based Screening of the Constituents of Calotropis procera Identifies Potential Inhibitors of Diabetes Mellitus Target Alpha Glucosidase. PMID:35723349
Network pharmacological analysis of active components of Tongqiao Huoxue Decoction in the treatment of intracerebral hemorrhage. PMID:35722393
Identifying RO9021 as a Potential Inhibitor of PknG from Mycobacterium tuberculosis: Combinative Computational and In Vitro Studies. PMID:35721990
Understanding the Mannose Transfer Mechanism of Mycobacterial Phosphatidyl-myo-inositol Mannosyltransferase A from Molecular Dynamics Simulations. PMID:35721920
Increased Frequency of Indels in Hypervariable Regions of SARS-CoV-2 Proteins-A Possible Signature of Adaptive Selection. PMID:35719386
Homology Modeling, de Novo Design of Ligands, and Molecular Docking Identify Potential Inhibitors of Leishmania donovani 24-Sterol Methyltransferase. PMID:35719359
Iron Deprivation Modulates the Exoproteome in Paracoccidioides brasiliensis. PMID:35719340
G4Boost: a machine learning-based tool for quadruplex identification and stability prediction. PMID:35717172
Repurposing benzbromarone as antifolate to develop novel antifungal therapy for Candida albicans. PMID:35716240
Ligand-based and structure-based studies to develop predictive models for SARS-CoV-2 main protease inhibitors through the 3d-qsar.com portal. PMID:35716228
Differential Expression of Genes Regulating Store-operated Calcium Entry in Conjunction With Mitochondrial Dynamics as Potential Biomarkers for Cancer: A Single-Cell RNA Analysis. PMID:35711942
Prediction and expression analysis of deleterious nonsynonymous SNPs of Arabidopsis ACD11 gene by combining computational algorithms and molecular docking approach. PMID:35709304
MAP segmentation in Bayesian hidden Markov models: a case study. PMID:35707511
RNABPDB: Molecular Modeling of RNA Structure-From Base Pair Analysis in Crystals to Structure Prediction. PMID:35705797
Simultaneous prediction of antibody backbone and side-chain conformations with deep learning. PMID:35704640
Gain and loss of TASK3 channel function and its regulation by novel variation cause KCNK9 imprinting syndrome. PMID:35698242
Enhanced Nuclear Magnetic Resonance Spectroscopy with Isotropic Mixing as a Pseudodimension. PMID:35695926
From the Wuhan-Hu-1 strain to the XD and XE variants: is targeting the SARS-CoV-2 spike protein still a pharmaceutically relevant option against COVID-19? PMID:35695095
Public Data Set of Protein-Ligand Dissociation Kinetic Constants for Quantitative Structure-Kinetics Relationship Studies. PMID:35694511
Unveiling the Possible Oryzalin-Binding Site in the α-Tubulin of Toxoplasma gondii. PMID:35694483
Global Analysis of Deep Learning Prediction Using Large-Scale In-House Kinome-Wide Profiling Data. PMID:35694454
HIV Transmembrane Glycoprotein Conserved Domains and Genetic Markers Across HIV-1 and HIV-2 Variants. PMID:35694284
CoeViz 2: Protein Graphs Derived from Amino Acid Covariance. PMID:35694032
Conserved coronavirus proteins as targets of broad-spectrum antivirals. PMID:35691424
NMR and dynamic light scattering give different diffusion information for short-living protein oligomers. Human serum albumin in water solutions of metal ions. PMID:35687130
Adamantane-Monoterpenoid Conjugates Linked via Heterocyclic Linkers Enhance the Cytotoxic Effect of Topotecan. PMID:35684313
Ibuprofen Favors Binding of Amyloid-β Peptide to Its Depot, Serum Albumin. PMID:35682848
Preparation of Novel Pyrazolo[4,3-e]tetrazolo[1,5-b][1,2,4]triazine Sulfonamides and Their Experimental and Computational Biological Studies. PMID:35682571
ERH Gene and Its Role in Cancer Cells. PMID:35677162
RNAsolo: a repository of cleaned PDB-derived RNA 3D structures. PMID:35674373
Network assisted analysis of de novo variants using protein-protein interaction information identified 46 candidate genes for congenital heart disease. PMID:35671298
Design and biological evaluation of substituted 5,7-dihydro-6H-indolo[2,3-c]quinolin-6-one as novel selective Haspin inhibitors. PMID:35670091
Integrated computational approach towards repurposing of antimalarial drug against SARS-CoV-2 main protease. PMID:35669793
HPMPdb: A machine learning-ready database of protein molecular phenotypes associated to human missense variants. PMID:35669450
AAV-vector based gene therapy for mitochondrial disease: progress and future perspectives. PMID:35668433
Neuroprotective effects of dimethyl fumarate against depression-like behaviors via astrocytes and microglia modulation in mice: possible involvement of the HCAR2/Nrf2 signaling pathway. PMID:35665831
GWYRE: A Resource for Mapping Variants onto Experimental and Modeled Structures of Human Protein Complexes. PMID:35662458
Structural landscapes of PPI interfaces. PMID:35656714
Antibody homotypic interactions are encoded by germline light chain complementarity determining region 2. PMID:35653561
Cyclization and Docking Protocol for Cyclic Peptide-Protein Modeling Using HADDOCK2.4. PMID:35652781
BETA: a comprehensive benchmark for computational drug-target prediction. PMID:35649342
Racemic crystal structures of A-DNA duplexes. PMID:35647918
Allantodapsone is a Pan-Inhibitor of Staphylococcus aureus Adhesion to Fibrinogen, Loricrin, and Cytokeratin 10. PMID:35647689
Exploring the Binding Mechanism of a Supramolecular Tweezer CLR01 to 14-3-3σ Protein via Well-Tempered Metadynamics. PMID:35646830
Resolution and characterization of contributions of select protein and coupled solvent configurational fluctuations to radical rearrangement catalysis in coenzyme B12-dependent ethanolamine ammonia-lyase. PMID:35644173
Characterizing and explaining the impact of disease-associated mutations in proteins without known structures or structural homologs. PMID:35641150
PADLOC: a web server for the identification of antiviral defence systems in microbial genomes. PMID:35639517
GrAfSS: a webserver for substructure similarity searching and comparisons in the structures of proteins and RNA. PMID:35639505
Dataset of normalized probability distributions of virtual bond lengths, bond angles, and dihedral angles for the coarse-grained single-stranded DNA structures. PMID:35637888
Parallel multi-swarm cooperative particle swarm optimization for protein-ligand docking and virtual screening. PMID:35637537
High-throughput virtual screening of small-molecule inhibitors targeting immune cell checkpoints to discover new immunotherapeutics for human diseases. PMID:35633442
Molecular Characterization and Identification of Potential Inhibitors for 'E' Protein of Dengue Virus. PMID:35632682
Design and Synthesis of Novel Bis-Imidazolyl Phenyl Butadiyne Derivatives as HCV NS5A Inhibitors. PMID:35631457
Machine-Learning Guided Discovery of Bioactive Inhibitors of PD1-PDL1 Interaction. PMID:35631439
Network Pharmacology Approach for Medicinal Plants: Review and Assessment. PMID:35631398
New Potential Pharmacological Targets of Plant-Derived Hydroxyanthraquinones from Rubia spp. PMID:35630751
Epithelial Sodium Channel Inhibition by Amiloride Addressed with THz Spectroscopy and Molecular Modeling. PMID:35630748
Revisiting DNA Sequence-Dependent Deformability in High-Resolution Structures: Effects of Flanking Base Pairs on Dinucleotide Morphology and Global Chain Configuration. PMID:35629425
Consensus Enolase of Trypanosoma Cruzi: Evaluation of Their Immunogenic Properties Using a Bioinformatics Approach. PMID:35629412
The Search for Cryptic L-Rhamnosyltransferases on the Sporothrix schenckii Genome. PMID:35628784
Molecular Dynamics Simulations Reveal Structural Interconnections within Sec14-PH Bipartite Domain from Human Neurofibromin. PMID:35628517
Complex Mutation Pattern of Omicron BA.2: Evading Antibodies without Losing Receptor Interactions. PMID:35628343
Computational Saturation Mutagenesis to Investigate the Effects of Neurexin-1 Mutations on AlphaFold Structure. PMID:35627176
Functional Dynamics of Substrate Recognition in TEM Beta-Lactamase. PMID:35626612
Conformational Entropy as a Potential Liability of Computationally Designed Antibodies. PMID:35625644
Transmission of SARS-CoV-2 from humans to animals and potential host adaptation. PMID:35624123
Comprehensive binary interaction mapping of τ phosphotyrosine sites with SH2 domains in the human genome: Implications for the rational design of self-inhibitory phosphopeptides to target τ hyperphosphorylation signaling in Alzheimer's Disease. PMID:35622130
Potential of Natural Alkaloids From Jadwar (Delphinium denudatum) as Inhibitors Against Main Protease of COVID-19: A Molecular Modeling Approach. PMID:35620478
A novel low temperature active maltooligosaccharides-forming amylase from Bacillus koreensis HL12 as biocatalyst for maltooligosaccharide production. PMID:35615748
Molecular Mingling: Multimodal Predictions of Ligand Promiscuity in Pentameric Ligand-Gated Ion Channels. PMID:35615739
In Silico Study of Cucurbita maxima Compounds as Potential Therapeutics Against Schistosomiasis. PMID:35615403
Discovery of bioactive microbial gene products in inflammatory bowel disease. PMID:35614211
Computational analysis of missense filamin-A variants, including the novel p.Arg484Gln variant of two brothers with periventricular nodular heterotopia. PMID:35613087
SARS-CoV-2 accessory proteins ORF7a and ORF3a use distinct mechanisms to downregulate MHC-I surface expression. PMID:35611331
In-vitro and in-silico antibacterial activity of Azadirachta indica (Neem), methanolic extract, and identification of Beta.d-Mannofuranoside as a promising antibacterial agent. PMID:35610569
CSM-Potential: mapping protein interactions and biological ligands in 3D space using geometric deep learning. PMID:35609999
AlignMe: an update of the web server for alignment of membrane protein sequences. PMID:35609986
CB-Dock2: improved protein-ligand blind docking by integrating cavity detection, docking and homologous template fitting. PMID:35609983
Fine-mapping studies distinguish genetic risks for childhood- and adult-onset asthma in the HLA region. PMID:35606880
Opening opportunities for Kd determination and screening of MHC peptide complexes. PMID:35606511
Structure-Guided Synthesis of FK506 and FK520 Analogs with Increased Selectivity Exhibit In Vivo Therapeutic Efficacy against Cryptococcus. PMID:35604094
Multifaceted membrane binding head of the SARS-CoV-2 spike protein. PMID:35602928
Identification of a Potential mRNA-based Vaccine Candidate against the SARS-CoV-2 Spike Glycoprotein: A Reverse Vaccinology Approach. PMID:35601809
Immunoinformatic paradigm predicts macrophage and T-cells epitope responses against globally conserved spike fragments of SARS CoV-2 for universal vaccination. PMID:35597120
Inhibition of the CDK2 and Cyclin A complex leads to autophagic degradation of CDK2 in cancer cells. PMID:35595767
The potential effects and mechanisms of hispidulin in the treatment of diabetic retinopathy based on network pharmacology. PMID:35590353
Understanding structural variability in proteins using protein structural networks. PMID:35586857
Evaluation of xanthene-appended quinoline hybrids as potential leads against antimalarial drug targets. PMID:35583686
Evolution of tunnels in α/β-hydrolase fold proteins-What can we learn from studying epoxide hydrolases? PMID:35580137
DOCKGROUND membrane protein-protein set. PMID:35580077
The potential effects and mechanisms of hispidulin in the treatment of diabetic retinopathy based on network pharmacology. PMID:35590353
Understanding structural variability in proteins using protein structural networks. PMID:35586857
Evaluation of xanthene-appended quinoline hybrids as potential leads against antimalarial drug targets. PMID:35583686
Evolution of tunnels in α/β-hydrolase fold proteins-What can we learn from studying epoxide hydrolases? PMID:35580137
DOCKGROUND membrane protein-protein set. PMID:35580077
SWORD2: hierarchical analysis of protein 3D structures. PMID:35580056
Repurposing the natural compounds as potential therapeutic agents for COVID-19 based on the molecular docking study of the main protease and the receptor-binding domain of spike protein. PMID:35578055
A genome-wide scan of wastewater E. coli for genes under positive selection: focusing on mechanisms of antibiotic resistance. PMID:35577863
Correlations from structure and phylogeny combine constructively in the inference of protein partners from sequences. PMID:35576238
System-Wide Analysis of the GATC-Binding Nucleoid-Associated Protein Gbn and Its Impact on Streptomyces Development. PMID:35575488
InterPepScore: A Deep Learning Score for Improving the FlexPepDock Refinement Protocol. PMID:35575349
Integrated Whole-Transcriptome Profiling and Bioinformatics Analysis of the Polypharmacological Effects of Ganoderic Acid Me in Colorectal Cancer Treatment. PMID:35574354
Identification of Phosphorylation and Other Post-Translational Modifications in the Central C4C5 Domains of Murine Cardiac Myosin Binding Protein C. PMID:35573219
Multiple-Allele MHC Class II Epitope Engineering by a Molecular Dynamics-Based Evolution Protocol. PMID:35572587
Methicillin-Resistant Staphylococcus aureus: Docking-Based Virtual Screening and Molecular Dynamics Simulations to Identify Potential Penicillin-Binding Protein 2a Inhibitors from Natural Flavonoids. PMID:35571353
Modulation of Tumor Immune Microenvironment and Prognostic Value of Ferroptosis-Related Genes, and Candidate Target Drugs in Glioblastoma Multiforme. PMID:35571123
Inhibitory effect of lignin on the hydrolysis of xylan by thermophilic and thermolabile GH11 xylanases. PMID:35568899
Accelerating AutoDock Vina with GPUs. PMID:35566391
Biocomputational Assessment of Natural Compounds as a Potent Inhibitor to Quorum Sensors in Ralstonia solanacearum. PMID:35566383
7-Aminoalkoxy-Quinazolines from Epigenetic Focused Libraries Are Potent and Selective Inhibitors of DNA Methyltransferase 1. PMID:35566242
In Silico Molecular Docking Analysis of Karanjin against Alzheimer's and Parkinson's Diseases as a Potential Natural Lead Molecule for New Drug Design, Development and Therapy. PMID:35566187
Identification of Mtb GlmU Uridyltransferase Domain Inhibitors by Ligand-Based and Structure-Based Drug Design Approaches. PMID:35566155
Development of Neuropeptide Y and Cell-Penetrating Peptide MAP Adsorbed onto Lipid Nanoparticle Surface. PMID:35566093
Novel Inhibitors of 2'-O-Methyltransferase of the SARS-CoV-2 Coronavirus. PMID:35566072
Recent Advances in Application of Computer-Aided Drug Design in Anti-Influenza A Virus Drug Discovery. PMID:35563129
The Multifaceted Role of GPCRs in Amyotrophic Lateral Sclerosis: A New Therapeutic Perspective? PMID:35562894
Coarse-graining protein structures into their dynamic communities with DCI, a dynamic community identifier. PMID:35561187
Drugsniffer: An Open Source Workflow for Virtually Screening Billions of Molecules for Binding Affinity to Protein Targets. PMID:35559261
Visualization of Topological Pharmacophore Space with Graph Edit Distance. PMID:35559135
Molecular dynamics derived life times of active substrate binding poses explain K M of laccase mutants. PMID:35558910
Molecular modeling provides a structural basis for PERK inhibitor selectivity towards RIPK1. PMID:35558862
Complex Loop Dynamics Underpin Activity, Specificity, and Evolvability in the (βα)8 Barrel Enzymes of Histidine and Tryptophan Biosynthesis. PMID:35557756
GeomBD3: Brownian Dynamics Simulation Software for Biological and Engineered Systems. PMID:35549473
Understanding the inhibitory mechanism of tea polyphenols against tyrosinase using fluorescence spectroscopy, cyclic voltammetry, oximetry, and molecular simulations. PMID:35542029
Egress and invasion machinery of malaria: an in-depth look into the structural and functional features of the flap dynamics of plasmepsin IX and X. PMID:35541758
The effect of the intramolecular C-H⋯O interactions on the conformational preferences of bis-arylsulfones - 5-HT6 receptor antagonists and beyond. PMID:35541096
A structural dissection of protein-RNA interactions based on different RNA base areas of interfaces. PMID:35540439
Protein secondary structure prediction with context convolutional neural network. PMID:35540205
A machine learning approach towards the prediction of protein-ligand binding affinity based on fundamental molecular properties. PMID:35539386
Discovery of acylphloroglucinol-based meroterpenoid enantiomers as KSHV inhibitors from Hypericum japonicum. PMID:35539193
The pocketome of G-protein-coupled receptors reveals previously untargeted allosteric sites. PMID:35538063
Computational study and design of effective siRNAs to silence structural proteins associated genes of Indian SARS-CoV-2 strains. PMID:35537364
Synthesis, antimicrobial, molecular docking and molecular dynamics studies of lauroyl thymidine analogs against SARS-CoV-2: POM study and identification of the pharmacophore sites. PMID:35533581
SARS-CoV-2 Delta Variant Decreases Nanobody Binding and ACE2 Blocking Effectivity. PMID:35533364
Synthesis of novel benzopyran-connected pyrimidine and pyrazole derivatives via a green method using Cu(ii)-tyrosinase enzyme catalyst as potential larvicidal, antifeedant activities. PMID:35530060
In Vivo Bioactivities of Hoya parasitica (Wall.) and In Silico Study against Cyclooxygenase Enzymes. PMID:35528171
NMR Assignment through Linear Programming. PMID:35528138
TeachOpenCADD 2022: open source and FAIR Python pipelines to assist in structural bioinformatics and cheminformatics research. PMID:35524571
iFeatureOmega: an integrative platform for engineering, visualization and analysis of features from molecular sequences, structural and ligand data sets. PMID:35524557
Thermostability mechanisms of β-agarase by analyzing its structure through molecular dynamics simulation. PMID:35524019
Network pharmacology of iridoid glycosides from Eucommia ulmoides Oliver against osteoporosis. PMID:35523810
Contribution of hydrophobic interactions to protein mechanical stability. PMID:35521554
Antiviral agents against COVID-19: structure-based design of specific peptidomimetic inhibitors of SARS-CoV-2 main protease. PMID:35520818
Network Pharmacology and Comparative Transcriptome Reveals Biotargets and Mechanisms of Curcumol Treating Lung Adenocarcinoma Patients With COVID-19. PMID:35520289
Accelerating the repurposing of FDA-approved drugs against coronavirus disease-19 (COVID-19). PMID:35519188
Synthesis, biological evaluation, and in silico studies of novel chalcone- and pyrazoline-based 1,3,5-triazines as potential anticancer agents. PMID:35519030
Drug-target affinity prediction using graph neural network and contact maps. PMID:35517730
Orientation effects on the nanoscale adsorption behavior of bone morphogenetic protein-2 on hydrophilic silicon dioxide. PMID:35517634
Consensus virtual screening of dark chemical matter and food chemicals uncover potential inhibitors of SARS-CoV-2 main protease. PMID:35517466
The catalytic influence of phosphotungstic acid-functionalized Fe3O4 MNPs blended with TiO2 on the synthesis of novel spiro-acridines and the evaluation of their medicinal potential through molecular docking studies. PMID:35517166
pDobz/pDobb protected diaminodiacid as a novel building block for peptide disulfide-bond mimic synthesis. PMID:35515921
A database of calculated solution parameters for the AlphaFold predicted protein structures. PMID:35513443
Licoflavone A Suppresses Gastric Cancer Growth and Metastasis by Blocking the VEGFR-2 Signaling Pathway. PMID:35509849
Comparative analysis of web-based programs for single amino acid substitutions in proteins. PMID:35507592
A Synthetic Gene Library Yields a Previously Unknown Glycoside Phosphorylase That Degrades and Assembles Poly-β-1,3-GlcNAc, Completing the Suite of β-Linked GlcNAc Polysaccharides. PMID:35505869
Efficient 3D conformer generation of cyclic peptides formed by a disulfide bond. PMID:35505401
Post-translational modification patterns on β-myosin heavy chain are altered in ischemic and nonischemic human hearts. PMID:35502901
Improved furfural tolerance in Escherichia coli mediated by heterologous NADH-dependent benzyl alcohol dehydrogenases. PMID:35502833
In silico bioprospecting of taraxerol as a main protease inhibitor of SARS-CoV-2 to develop therapy against COVID-19. PMID:35502321
A topological data analytic approach for discovering biophysical signatures in protein dynamics. PMID:35500014
Neuroprotective potential of terpenoid-rich extracts from orange juice by-products obtained by pressurized liquid extraction. PMID:35498984
Machine learning model for fast prediction of the natural frequencies of protein molecules. PMID:35498827
The FUSION protein crystallization screen. PMID:35497656
Synthesis, characterization, in silico molecular docking, and antibacterial activities of some new nitrogen-heterocyclic analogues based on a p-phenolic unit. PMID:35496342
Monte Carlo simulations using PELE to identify a protein-protein inhibitor binding site and pose. PMID:35493910
Theoretical insights into the effect of halogenated substituent on the electronic structure and spectroscopic properties of the favipiravir tautomeric forms and its implications for the treatment of COVID-19. PMID:35493173
ProteinsPlus: a comprehensive collection of web-based molecular modeling tools. PMID:35489057
Matching protein surface structural patches for high-resolution blind peptide docking. PMID:35482919
Electrostatic fingerprints of catalytically active amino acids in enzymes. PMID:35481659
Latin American databases of natural products: biodiversity and drug discovery against SARS-CoV-2. PMID:35481202
Experiences From Developing Software for Large X-Ray Crystallography-Driven Protein-Ligand Studies. PMID:35480897
Immunoinformatics-guided design of a multi-epitope vaccine based on the structural proteins of severe acute respiratory syndrome coronavirus 2. PMID:35480208
The polyphenolic phytoalexin polydatin inhibits amyloid aggregation of recombinant human prion protein. PMID:35479435
In Silico Identification and Characterization of a Hypothetical Protein From Rhodobacter capsulatus Revealing S-Adenosylmethionine-Dependent Methyltransferase Activity. PMID:35478993
LM-GVP: an extensible sequence and structure informed deep learning framework for protein property prediction. PMID:35477726
Linking hIAPP misfolding and aggregation with type 2 diabetes mellitus: a structural perspective. PMID:35475576
Deciphering Isoniazid Drug Resistance Mechanisms on Dimeric Mycobacterium tuberculosis KatG via Post-molecular Dynamics Analyses Including Combined Dynamic Residue Network Metrics. PMID:35474779
Bacterial-type ferroxidase tunes iron-dependent phosphate sensing during Arabidopsis root development. PMID:35472311
Δ-Quantum machine-learning for medicinal chemistry. PMID:35470831
The predictive potential of different molecular markers linked to amikacin susceptibility phenotypes in Pseudomonas aeruginosa. PMID:35468158
Identification of potential andrographolide-based drug candidate against Keap1-Nrf2 pathway through rigorous cheminformatics screening. PMID:35467270
Resolution and characterization of confinement- and temperature-dependent dynamics in solvent phases that surround proteins in frozen aqueous solution by using spin-probe EPR spectroscopy. PMID:35465922
The Evolution of Intein-Based Affinity Methods as Reflected in 30 years of Patent History. PMID:35463948
Irisin Suppresses Nicotine-Mediated Atherosclerosis by Attenuating Endothelial Cell Migration, Proliferation, Cell Cycle Arrest, and Cell Senescence. PMID:35463776
The SARS-CoV-2 helicase as a target for antiviral therapy: Identification of potential small molecule inhibitors by in silico modelling. PMID:35462185
Probing the competitive inhibitor efficacy of frog-skin alpha helical AMPs identified against ACE2 binding to SARS-CoV-2 S1 spike protein as therapeutic scaffold to prevent COVID-19. PMID:35461388
Discovery of Bispecific Lead Compounds from Azadirachta indica against ZIKA NS2B-NS3 Protease and NS5 RNA Dependent RNA Polymerase Using Molecular Simulations. PMID:35458761
Docking, Binding Free Energy Calculations and In Vitro Characterization of Pyrazine Linked 2-Aminobenzamides as Novel Class I Histone Deacetylase (HDAC) Inhibitors. PMID:35458724
Molecular Modeling and Experimental Evaluation of Non-Chiral Components of Bergamot Essential Oil with Inhibitory Activity against Human Monoamine Oxidases. PMID:35458667
Drug Resistance Mechanism of M46I-Mutation-Induced Saquinavir Resistance in HIV-1 Protease Using Molecular Dynamics Simulation and Binding Energy Calculation. PMID:35458427
Novel Mutations in Putative Nicotinic Acid Phosphoribosyltransferases of Mycobacterium tuberculosis and Their Effect on Protein Thermodynamic Properties. PMID:35458373
Computer Simulations and Network-Based Profiling of Binding and Allosteric Interactions of SARS-CoV-2 Spike Variant Complexes and the Host Receptor: Dissecting the Mechanistic Effects of the Delta and Omicron Mutations. PMID:35457196
Theophylline: Old Drug in a New Light, Application in COVID-19 through Computational Studies. PMID:35456985
New Genetic Bomb Trigger: Design, Synthesis, Molecular Dynamics Simulation, and Biological Evaluation of Novel BIBR1532-Related Analogs Targeting Telomerase against Non-Small Cell Lung Cancer. PMID:35455478
Integrating Network Pharmacology and Molecular Docking Approaches to Decipher the Multi-Target Pharmacological Mechanism of Abrus precatorius L. Acting on Diabetes. PMID:35455411
Improvement of Biocatalytic Properties and Cytotoxic Activity of L-Asparaginase from Rhodospirillum rubrum by Conjugation with Chitosan-Based Cationic Polyelectrolytes. PMID:35455403
Synthesis and Effect of Conformationally Locked Carbocyclic Guanine Nucleotides on Dynamin. PMID:35454173
Mutational Effect of Some Major COVID-19 Variants on Binding of the S Protein to ACE2. PMID:35454161
Distribution of Charged Residues Affects the Average Size and Shape of Intrinsically Disordered Proteins. PMID:35454150
Computational prediction of potential inhibitors for SARS-COV-2 main protease based on machine learning, docking, MM-PBSA calculations, and metadynamics. PMID:35452494
Genetic diversity of the melanocortin-1 receptor in an admixed population of Rio de Janeiro: Structural and functional impacts of Cys35Tyr variant. PMID:35452484
Neutron scattering maps the higher-order assembly of NADPH-dependent assimilatory sulfite reductase. PMID:35443926
Hepcidin is potential regulator for renin activity. PMID:35442992
Immunoinformatics approach of epitope prediction for SARS-CoV-2. PMID:35441904
Mining anion-aromatic interactions in the Protein Data Bank. PMID:35440982
LoopGrafter: a web tool for transplanting dynamical loops for protein engineering. PMID:35438789
A path-based analysis of infected cell line and COVID-19 patient transcriptome reveals novel potential targets and drugs against SARS-CoV-2. PMID:35434729
The protein folding rate and the geometry and topology of the native state. PMID:35430582
Expanding the clinical-pathological and genetic spectrum of RYR1-related congenital myopathies with cores and minicores: an Italian population study. PMID:35428369
Mycobacterium tuberculosis requires SufT for Fe-S cluster maturation, metabolism, and survival in vivo. PMID:35427399
Design of a multi-epitope vaccine against SARS-CoV-2: immunoinformatic and computational methods. PMID:35425433
Phenylalanyl tRNA synthetase (PheRS) substrate mimics: design, synthesis, molecular dynamics and antimicrobial evaluation. PMID:35425259
Structure-based discovery and bio-evaluation of a cyclopenta[4,5]thieno[2,3-d]pyrimidin-4-one as a phosphodiesterase 10A inhibitor. PMID:35425186
Identification of aldehyde oxidase 3 as a binding protein for squid ink polysaccharides using magnetic nanoparticles. PMID:35424304
In silico exploration of lignin peroxidase for unraveling the degradation mechanism employing lignin model compounds. PMID:35423962
Epitope-imprinted polymers: applications in protein recognition and separation. PMID:35423617
Deciphering the structure of Arabidopsis thaliana 5-enol-pyruvyl-shikimate-3-phosphate synthase: An essential step toward the discovery of novel inhibitors to supersede glyphosate. PMID:35422967
MutCov: A pipeline for evaluating the effect of mutations in spike protein on infectivity and antigenicity of SARS-CoV-2. PMID:35421792
Epitope Identification and Designing a Potent Multi-epitope Vaccine Construct against SARS-CoV-2 Including the Emerging Variants. PMID:35418729
Identification and molecular characterization of a novel non-specific lipid transfer protein (TdLTP2) from durum wheat. PMID:35417502
Functional cross-species conservation of guanylate-binding proteins in innate immunity. PMID:35416510
Overcoming Multidrug Resistance (MDR): Design, Biological Evaluation and Molecular Modelling Studies of 2,4-Substituted Quinazoline Derivatives. PMID:35416421
Protein-Protein Binding Free Energy Predictions with the MM/PBSA Approach Complemented with the Gaussian-Based Method for Entropy Estimation. PMID:35415339
Sprayable nanomicelle hydrogels and inflammatory bowel disease patient cell chips for development of intestinal lesion-specific therapy. PMID:35415304
Towards the simulation of large scale protein-ligand interactions on NISQ-era quantum computers. PMID:35414867
Bioinformatics Screening of Potential Biomarkers from mRNA Expression Profiles to Discover Drug Targets and Agents for Cervical Cancer. PMID:35409328
Human Vitamin K Epoxide Reductase as a Target of Its Redox Protein. PMID:35409257
VHH Structural Modelling Approaches: A Critical Review. PMID:35409081
Transcription Factors with Targeting Potential in Gliomas. PMID:35409080
Assortment of Frontiers in Protein Science. PMID:35409045
In Silico Characterisation of the Late Embryogenesis Abundant (LEA) Protein Families and Their Role in Desiccation Tolerance in Ramonda serbica Panc. PMID:35408906
Potential Immunogenic Activity of Computationally Designed mRNA- and Peptide-Based Prophylactic Vaccines against MERS, SARS-CoV, and SARS-CoV-2: A Reverse Vaccinology Approach. PMID:35408772
SARS-CoV-2 spike protein-, main protease- and papain-like-protease-targeting peptides from seed proteins following gastrointestinal digestion: An in silico study. PMID:35403082
DUX4 is a multifunctional factor priming human embryonic genome activation. PMID:35402882
A Comprehensive Review of Computation-Based Metal-Binding Prediction Approaches at the Residue Level. PMID:35402609
Re-Expression of ERα and AR in Receptor Negative Endocrine Cancers via GSK3 Inhibition. PMID:35402240
Feasibility of Follow-Up Studies and Reclassification in Spinocerebellar Ataxia Gene Variants of Unknown Significance. PMID:35401678
Identification of bio-active food compounds as potential SARS-CoV-2 PLpro inhibitors-modulators via negative image-based screening and computational simulations. PMID:35395517
NeuralDock: Rapid and Conformation-Agnostic Docking of Small Molecules. PMID:35392534
Dynamic coupling of residues within proteins as a mechanistic foundation of many enigmatic pathogenic missense variants. PMID:35389981
Network Pharmacology Integrated with Transcriptomics Deciphered the Potential Mechanism of Codonopsis pilosula against Hepatocellular Carcinoma. PMID:35388300
Allergological Importance of Invertebrate Glutathione Transferases in Tropical Environments. PMID:35387058
In Silico Prediction of Epitopes in Virulence Proteins of Mycobacterium ulcerans for Vaccine Designing. PMID:35386432
Computer-aided engineering of staphylokinase toward enhanced affinity and selectivity for plasmin. PMID:35386102
Real-time structure search and structure classification for AlphaFold protein models. PMID:35383281
When are two hydrogen bonds better than one? Accurate first-principles models explain the balance of hydrogen bond donors and acceptors found in proteins. PMID:35382134
CryoETGAN: Cryo-Electron Tomography Image Synthesis via Unpaired Image Translation. PMID:35370760
Atorvastatin Effectively Inhibits Ancestral and Two Emerging Variants of SARS-CoV-2 in vitro. PMID:35369500
Tree diet: reducing the treewidth to unlock FPT algorithms in RNA bioinformatics. PMID:35366923
The potential mechanism of Bupleurum against anxiety was predicted by network pharmacology study and molecular docking. PMID:35366129
AF2Complex predicts direct physical interactions in multimeric proteins with deep learning. PMID:35365655
Current progress and open challenges for applying deep learning across the biosciences. PMID:35365602
Protein dynamics developments for the large scale and cryoEM: case study of ProDy 2.0. PMID:35362464
Variations in antibody repertoires correlate with vaccine responses. PMID:35361626
SAWRPI: A Stacking Ensemble Framework With Adaptive Weight for Predicting ncRNA-Protein Interactions Using Sequence Information. PMID:35360836
Identifying Active Substances and the Pharmacological Mechanism of Houttuynia cordata Thunb. in Treating Radiation-Induced Lung Injury Based on Network Pharmacology and Molecular Docking Verification. PMID:35360660
Investigation of the structural dynamics of a knotted protein and its unknotted analog using molecular dynamics. PMID:35357594
Generating 3D molecules conditional on receptor binding sites with deep generative models. PMID:35356675
Target Specific Inhibition of Protein Tyrosine Kinase in Conjunction With Cancer and SARS-COV-2 by Olive Nutraceuticals. PMID:35356629
Kinase domain autophosphorylation rewires the activity and substrate specificity of CK1 enzymes. PMID:35353987
Engineering of phenylalanine dehydrogenase from Thermoactinomyces intermedius for the production of a novel homoglutamate. PMID:35353822
Development and Validation of Fluorinated, Aromatic Amino Acid Parameters for Use with the AMBER ff15ipq Protein Force Field. PMID:35352936
Structure-based design and construction of a synthetic phage display nanobody library. PMID:35351202
Adding hydrogen atoms to molecular models via fragment superimposition. PMID:35351165
The Structural Determinants of Intra-Protein Compensatory Substitutions. PMID:35349721
RNAspider: a webserver to analyze entanglements in RNA 3D structures. PMID:35349710
Protein design via deep learning. PMID:35348602
Synthesis, spectroscopic characterization of novel phthalimides derivatives bearing a 1,2,3-triazole unit and examination as potential SARS-CoV-2 inhibitors via in silico studies. PMID:35345413
emDNA - A Tool for Modeling Protein-decorated DNA Loops and Minicircles at the Base-pair Step Level. PMID:35341743
E-Volve: understanding the impact of mutations in SARS-CoV-2 variants spike protein on antibodies and ACE2 affinity through patterns of chemical interactions at protein interfaces. PMID:35341044
The inner side of yeast PCNA contributes to genome stability by mediating interactions with Rad18 and the replicative DNA polymerase δ. PMID:35338218
Sodium or Not Sodium: Should Its Presence Affect the Accuracy of Pose Prediction in Docking GPCR Antagonists? PMID:35337144
Rethinking Protein Drug Design with Highly Accurate Structure Prediction of Anti-CRISPR Proteins. PMID:35337108
Major Achievements in the Design of Quadruplex-Interactive Small Molecules. PMID:35337098
Conserved Targets to Prevent Emerging Coronaviruses. PMID:35336969
Aspects of Biological Replication and Evolution Independent of the Central Dogma: Insights from Protein-Free Vesicular Transformations and Protein-Mediated Membrane Remodeling. PMID:35333977
Design of protein-binding proteins from the target structure alone. PMID:35332283
Fragment-based virtual screening discovers potential new Plasmodium PI4KIIIβ ligands. PMID:35331319
Next-Generation Molecular Discovery: From Bottom-Up In Vivo and In Vitro Approaches to In Silico Top-Down Approaches for Therapeutics Neogenesis. PMID:35330114
Devising Bone Molecular Models at the Nanoscale: From Usual Mineralized Collagen Fibrils to the First Bone Fibers Including Hydroxyapatite in the Extra-Fibrillar Volume. PMID:35329726
Challenges with Simulating Modified RNA: Insights into Role and Reciprocity of Experimental and Computational Approaches. PMID:35328093
Stitchr: stitching coding TCR nucleotide sequences from V/J/CDR3 information. PMID:35325179
Fast protein structure comparison through effective representation learning with contrastive graph neural networks. PMID:35324898
A Benchmark Dataset for Evaluating Practical Performance of Model Quality Assessment of Homology Models. PMID:35324806
A Computational Understanding of Inter-Individual Variability in CYP2D6 Activity to Investigate the Impact of Missense Mutations on Ochratoxin A Metabolism. PMID:35324704
In Silico Evaluation of Antifungal Compounds from Marine Sponges against COVID-19-Associated Mucormycosis. PMID:35323514
Atomistic mechanisms of human TRPA1 activation by electrophile irritants through molecular dynamics simulation and mutual information analysis. PMID:35322090
Omicron Variant of SARS-CoV-2 Virus: In Silico Evaluation of the Possible Impact on People Affected by Diabetes Mellitus. PMID:35321335
Complete Genome Sequence of Stenotrophomonas maltophilia Podophage Piffle. PMID:35319268
Lightweight ProteinUnet2 network for protein secondary structure prediction: a step towards proper evaluation. PMID:35317722
Protein-ligand binding affinity prediction based on profiles of intermolecular contacts. PMID:35317230
Elevation of ADAM12 facilitates tumor progression by enhancing metastasis and immune infiltration in gastric cancer. PMID:35315496
Immunogenic Epitope-Based Vaccine Prediction from Surface Glycoprotein of MERS-CoV by Deploying Immunoinformatics Approach. PMID:35313444
Identifying potential natural inhibitors of Brucella melitensis Methionyl-tRNA synthetase through an in-silico approach. PMID:35312681
Ligand binding remodels protein side-chain conformational heterogeneity. PMID:35312477
Interaction Analysis of the Spike Protein of Delta and Omicron Variants of SARS-CoV-2 with hACE2 and Eight Monoclonal Antibodies Using the Fragment Molecular Orbital Method. PMID:35312321
Immunotherapeutic Value of MAP1LC3C and Its Candidate FDA-Approved Drugs Identified by Pan-Cancer Analysis, Virtual Screening and Sensitivity Analysis. PMID:35308199
Systematic analysis and molecular profiling of EGFR allosteric inhibitor cross-reactivity across the proto-oncogenic ErbB family kinases by integrating dynamics simulation, energetics calculation and biochemical assay. PMID:35307752
Cardiac protection by pirfenidone after myocardial infarction: a bioinformatic analysis. PMID:35304529
Predicting residues involved in anti-DNA autoantibodies with limited neural networks. PMID:35303216
Molecular dynamics simulation or structure refinement of proteins: are solvent molecules required? A case study using hen lysozyme. PMID:35303138
Effect of dopamine-functionalization, charge and pH on protein corona formation around TiO2 nanoparticles. PMID:35302136
A novel AMPK activator shows therapeutic potential in hepatocellular carcinoma by suppressing HIF1α-mediated aerobic glycolysis. PMID:35298869
Computational Evolution Protocol for Peptide Design. PMID:35298821
Structural Prediction of Peptide-MHC Binding Modes. PMID:35298818
Tools for Characterizing Proteins: Circular Variance, Mutual Proximity, Chameleon Sequences, and Subsequence Propensities. PMID:35298807
Machine Learning Prediction of Antimicrobial Peptides. PMID:35298806
Self-assembled nanoparticle-enzyme aggregates enhance functional protein production in pure transcription-translation systems. PMID:35298538
Vaccine Candidate Against COVID-19 Based on Structurally Modified Plant Virus as an Adjuvant. PMID:35295298
Progress and challenges for the machine learning-based design of fit-for-purpose monoclonal antibodies. PMID:35293269
Mapping the sequence specificity of heterotypic amyloid interactions enables the identification of aggregation modifiers. PMID:35292653
Evolution of the Automatic Rhodopsin Modeling (ARM) Protocol. PMID:35291019
Quantifying and comparing radiation damage in the Protein Data Bank. PMID:35288575
Machine learning prediction of 3CLpro SARS-CoV-2 docking scores. PMID:35288359
Protecting effect of emodin in experimental autoimmune encephalomyelitis mice by inhibiting microglia activation and inflammation via Myd88/PI3K/Akt/NF-κB signalling pathway. PMID:35287559
A twist in the road less traveled: The AMBER ff15ipq-m force field for protein mimetics. PMID:35287464
Large-scale design and refinement of stable proteins using sequence-only models. PMID:35286324
Evaluation of the Prognostic Relevance of Differential Claudin Gene Expression Highlights Claudin-4 as Being Suppressed by TGFβ1 Inhibitor in Colorectal Cancer. PMID:35281827
HLA-G and the MHC Cusp Theory. PMID:35281038
A highly sensitive cell-based luciferase assay for high-throughput automated screening of SARS-CoV-2 nsp5/3CLpro inhibitors. PMID:35278581
Genome-wide pharmacogenetics of anti-drug antibody response to bococizumab highlights key residues in HLA DRB1 and DQB1. PMID:35277540
Computational identification of host genomic biomarkers highlighting their functions, pathways and regulators that influence SARS-CoV-2 infections and drug repurposing. PMID:35277538
Discovery and In Vivo Proof of Concept of a Highly Potent Dual Inhibitor of Soluble Epoxide Hydrolase and Acetylcholinesterase for the Treatment of Alzheimer's Disease. PMID:35271276
Conformational Dynamics of the Soluble and Membrane-Bound Forms of Interleukin-1 Receptor Type-1: Insights into Linker Flexibility and Domain Orientation. PMID:35269739
Identification and Quantitation of Bioactive and Taste-Related Dipeptides in Low-Salt Dry-Cured Ham. PMID:35269650
Nanoscale Topographical Effects on the Adsorption Behavior of Bone Morphogenetic Protein-2 on Graphite. PMID:35269575
Potential of the Compounds from Bixa orellana Purified Annatto Oil and Its Granules (Chronic®) against Dyslipidemia and Inflammatory Diseases: In Silico Studies with Geranylgeraniol and Tocotrienols. PMID:35268686
Identification of the potential mechanism of Radix pueraria in colon cancer based on network pharmacology. PMID:35260672
Polyphenols as potential enhancers of stem cell therapy against neurodegeneration. PMID:35259814
Design and various in silico studies of the novel curcumin derivatives as potential candidates against COVID-19 -associated main enzymes. PMID:35259661
Chemical composition and therapeutic mechanism of Xuanbai Chengqi Decoction in the treatment of COVID-19 by network pharmacology, molecular docking and molecular dynamic analysis. PMID:35258759
ID23-2: an automated and high-performance microfocus beamline for macromolecular crystallography at the ESRF. PMID:35254323
Microsecond Backbone Motions Modulate the Oligomerization of the DNAJB6 Chaperone. PMID:35247211
Implication of in silico studies in the search for novel inhibitors against SARS-CoV-2. PMID:35244237
Conformational dynamics promotes disordered regions from function-dispensable to essential in evolved site-specific DNA recombinases. PMID:35242289
Conformational Variation in Enzyme Catalysis: A Structural Study on Catalytic Residues. PMID:35240125
Modeling multi-scale data via a network of networks. PMID:35238343
Genome-Wide Association Study-Guided Exome Rare Variant Burden Analysis Identifies IL1R1 and CD3E as Potential Autoimmunity Risk Genes for Celiac Disease. PMID:35237542
The SARS-CoV-2 spike reversibly samples an open-trimer conformation exposing novel epitopes. PMID:35236990
Secondary structural ensembles of the SARS-CoV-2 RNA genome in infected cells. PMID:35236847
An advanced network pharmacology study to explore the novel molecular mechanism of Compound Kushen Injection for treating hepatocellular carcinoma by bioinformatics and experimental verification. PMID:35236335
SARS-CoV-2 Nsp13 encodes for an HLA-E-stabilizing peptide that abrogates inhibition of NKG2A-expressing NK cells. PMID:35235832
Novel mutation in hexokinase 2 confers resistance to 2-deoxyglucose by altering protein dynamics. PMID:35235554
A simple technique to classify diffraction data from dynamic proteins according to individual polymorphs. PMID:35234141
PSnpBind: a database of mutated binding site protein-ligand complexes constructed using a multithreaded virtual screening workflow. PMID:35227289
Screening the components of Saussurea involucrata for novel targets for the treatment of NSCLC using network pharmacology. PMID:35227278
Compounds targeting GPI biosynthesis or N-glycosylation are active against Plasmodium falciparum. PMID:35222844
Evaluation of protein descriptors in computer-aided rational protein engineering tasks and its application in property prediction in SARS-CoV-2 spike glycoprotein. PMID:35222841
Identification of Hypericin as a Candidate Repurposed Therapeutic Agent for COVID-19 and Its Potential Anti-SARS-CoV-2 Activity. PMID:35222340
Combatting future variants of SARS-CoV-2 using an in-silico peptide vaccine approach by targeting the spike protein. PMID:35221449
Searching for a mechanistic description of pairwise epistasis in protein systems. PMID:35218569
Allosteric Determinants of the SARS-CoV-2 Spike Protein Binding with Nanobodies: Examining Mechanisms of Mutational Escape and Sensitivity of the Omicron Variant. PMID:35216287
EMBER-Embedding Multiple Molecular Fingerprints for Virtual Screening. PMID:35216273
Analysis of the Neutralizing Activity of Antibodies Targeting Open or Closed SARS-CoV-2 Spike Protein Conformations. PMID:35216194
Interferon-β Activity Is Affected by S100B Protein. PMID:35216109
Well Put Together-A Guide to Accessorizing with the Herpesvirus gH/gL Complexes. PMID:35215889
Re-Exploring the Ability of Common Docking Programs to Correctly Reproduce the Binding Modes of Non-Covalent Inhibitors of SARS-CoV-2 Protease Mpro. PMID:35215293
Capturing a Crucial 'Disorder-to-Order Transition' at the Heart of the Coronavirus Molecular Pathology-Triggered by Highly Persistent, Interchangeable Salt-Bridges. PMID:35214759
Isolation of Thioinosine and Butenolides from a Terrestrial Actinomycetes sp. GSCW-51 and Their in Silico Studies for Potential against SARS-CoV-2. PMID:35213767
Expansion of the 4-(Diethylamino)benzaldehyde Scaffold to Explore the Impact on Aldehyde Dehydrogenase Activity and Antiproliferative Activity in Prostate Cancer. PMID:35212533
Novel nitrite reductase domain structure suggests a chimeric denitrification repertoire in the phylum Chloroflexi. PMID:35212484
The Efficacy Mechanism of Epigallocatechin Gallate against Pre-Eclampsia based on Network Pharmacology and Molecular Docking. PMID:35211881
Using Steady-State Kinetics to Quantitate Substrate Selectivity and Specificity: A Case Study with Two Human Transaminases. PMID:35209187
New Blood Coagulation Factor XIIa Inhibitors: Molecular Modeling, Synthesis, and Experimental Confirmation. PMID:35209023
Alkaloid Profiling, Anti-Enzymatic and Antiproliferative Activity of the Endemic Chilean Amaryllidaceae Phycella cyrtanthoides. PMID:35208261
Phenolic Profile, Antioxidant and Enzyme Inhibition Properties of the Chilean Endemic Plant Ovidia pillopillo (Gay) Meissner (Thymelaeaceae). PMID:35208165
Computer Aided Drug Design Approach to Screen Phytoconstituents of Adhatoda vasica as Potential Inhibitors of SARS-CoV-2 Main Protease Enzyme. PMID:35207602
Searching for Low Probability Opening Events in a DNA Sliding Clamp. PMID:35207548
Analysis of Fluctuation in the Heme-Binding Pocket and Heme Distortion in Hemoglobin and Myoglobin. PMID:35207496
The Complex Biological Effects of Pectin: Galectin-3 Targeting as Potential Human Health Improvement? PMID:35204790
Hydroxamic Acid as a Potent Metal-Binding Group for Inhibiting Tyrosinase. PMID:35204163
Drug Repurposing Targeting Pseudomonas aeruginosa MvfR Using Docking, Virtual Screening, Molecular Dynamics, and Free-Energy Calculations. PMID:35203788
Dimerization of the Glucocorticoid Receptor and Its Importance in (Patho)physiology: A Primer. PMID:35203332
In vivo fluorescence lifetime imaging of macrophage intracellular metabolism during wound responses in zebrafish. PMID:35200139
Benchmarking ensemble docking methods in D3R Grand Challenge 4. PMID:35199221
Structural Comparison and Drug Screening of Spike Proteins of Ten SARS-CoV-2 Variants. PMID:35198984
Enzymatic activity of glycosyltransferase GLT8D1 promotes human glioblastoma cell migration. PMID:35198895
Fortilin interacts with TGF-β1 and prevents TGF-β receptor activation. PMID:35197550
Screening and identification of potential inhibitor for visceral leishmaniasis (VL) through computational analysis. PMID:35195803
Structural insights into inhibition of PRRSV Nsp4 revealed by structure-based virtual screening, molecular dynamics, and MM-PBSA studies. PMID:35193698
Outliers in SAR and QSAR: 4. effects of allosteric protein-ligand interactions on the classical quantitative structure-activity relationships. PMID:35192113
Using AnnoTree to Get More Assignments, Faster, in DIAMOND+MEGAN Microbiome Analysis. PMID:35191776
Dynamic disequilibrium-based pathogenicity model in mutated pyrin's B30.2 domain-Casp1/p20 complex. PMID:35190906
Concurrent Identification and Characterization of Protein Structure and Continuous Internal Dynamics with REDCRAFT. PMID:35187082
Librator: a platform for the optimized analysis, design, and expression of mutable influenza viral antigens. PMID:35183062
PyUUL provides an interface between biological structures and deep learning algorithms. PMID:35181656
In Silico and Ex Vivo Analyses of the Inhibitory Action of the Alzheimer Drug Posiphen and Primary Metabolites with Human Acetyl- and Butyrylcholinesterase Enzymes. PMID:35178511
Protein-protein interactions enhance the thermal resilience of SpyRing-cyclized enzymes: A molecular dynamic simulation study. PMID:35176056
Single Stabilizing Point Mutation Enables High-Resolution Co-Crystal Structures of the Adenosine A2A Receptor with Preladenant Conjugates. PMID:35174942
Sustained software development, not number of citations or journal choice, is indicative of accurate bioinformatic software. PMID:35172880
Evolutionary History of TOPIIA Topoisomerases in Animals. PMID:35165762
Structural insights into the Venus flytrap mechanosensitive ion channel Flycatcher1. PMID:35165281
Crystal Structure of H227A Mutant of Arginine Kinase in Daphnia magna Suggests the Importance of Its Stability. PMID:35164149
Autoxidation Products of the Methanolic Extract of the Leaves of Combretum micranthum Exert Antiviral Activity against Tomato Brown Rugose Fruit Virus (ToBRFV). PMID:35164024
Isolation, Characterization and In Silico Studies of Secondary Metabolites from the Whole Plant of Polygala inexpectata Peşmen & Erik. PMID:35163950
DrugDevCovid19: An Atlas of Anti-COVID-19 Compounds Derived by Computer-Aided Drug Design. PMID:35163948
Phytochemical Compound Screening to Identify Novel Small Molecules against Dengue Virus: A Docking and Dynamics Study. PMID:35163918
Novel Aurora A Kinase Inhibitor Fangchinoline Enhances Cisplatin-DNA Adducts and Cisplatin Therapeutic Efficacy in OVCAR-3 Ovarian Cancer Cells-Derived Xenograft Model. PMID:35163790
Influenza A Virus NS1 Protein Structural Flexibility Analysis According to Its Structural Polymorphism Using Computational Approaches. PMID:35163728
The Therapeutic Prospects of Targeting IL-1R1 for the Modulation of Neuroinflammation in Central Nervous System Disorders. PMID:35163653
Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. PMID:35163572
Docking and Molecular Dynamic of Microalgae Compounds as Potential Inhibitors of Beta-Lactamase. PMID:35163569
Slipknot or Crystallographic Error: A Computational Analysis of the Plasmodium falciparum DHFR Structural Folds. PMID:35163439
Mutations in human SARS-CoV-2 spike proteins, potential drug binding and epitope sites for COVID-19 therapeutics development. PMID:35156058
Editorial: Advances in Molecular Docking and Structure-Based Modelling. PMID:35155583
SOMSpec as a General Purpose Validated Self-Organising Map Tool for Rapid Protein Secondary Structure Prediction From Infrared Absorbance Data. PMID:35155377
CCR5 as a Coreceptor for Human Immunodeficiency Virus and Simian Immunodeficiency Viruses: A Prototypic Love-Hate Affair. PMID:35154162
Expression and Characterization of Relaxin Family Peptide Receptor 1 Variants. PMID:35153771
Nuclear genome-derived circular RNA circPUM1 localizes in mitochondria and regulates oxidative phosphorylation in esophageal squamous cell carcinoma. PMID:35153295
The tetrameric structure of Plasmodium falciparum phosphoglycerate mutase is critical for optimal enzymatic activity. PMID:35150741
PIPENN: Protein Interface Prediction from sequence with an Ensemble of Neural Nets. PMID:35150231
Genome Nexus: A Comprehensive Resource for the Annotation and Interpretation of Genomic Variants in Cancer. PMID:35148171
Polygenic risk impacts PDGFRA mutation penetrance in non-syndromic cleft lip and palate. PMID:35147171
A backbone-centred energy function of neural networks for protein design. PMID:35140398
Acipimox inhibits human carbonic anhydrases. PMID:35139721
Pathogenic variants in the human m6A reader YTHDC2 are associated with primary ovarian insufficiency. PMID:35138268
Solution structure and dynamics of the mitochondrial-targeted GTPase-activating protein (GAP) VopE by an integrated NMR/SAXS approach. PMID:35137487
Global conserved RBD fraction of SARS-CoV-2 S-protein with T500S mutation in silico significantly blocks ACE2 and rejects viral spike. PMID:35136839
Co-circulation of two SARS-CoV-2 variant strains within imported pet hamsters in Hong Kong. PMID:35135441
Inherent conformational plasticity in dsRBDs enables interaction with topologically distinct RNAs. PMID:35134335
PlantGF: an analysis and annotation platform for plant gene families. PMID:35134149
Innovative next-generation therapies in combating multi-drug-resistant and multi-virulent Escherichia coli isolates: insights from in vitro, in vivo, and molecular docking studies. PMID:35133473
Optimization of Cavity-Based Negative Images to Boost Docking Enrichment in Virtual Screening. PMID:35133138
Glyco-Steroidal Amphiphiles (GSAs) for Membrane Protein Structural Study. PMID:35129249
Cancer Chemopreventive Potential and Chemical Profiling of Euphorbia abyssinica Endowed with Docking Studies. PMID:35128266
Discovery of novel selective PI3Kγ inhibitors through combining machine learning-based virtual screening with multiple protein structures and bio-evaluation. PMID:35127160
Design & discovery of small molecule COVID-19 inhibitor via dual approach based virtual screening and molecular simulation studies. PMID:35125836
A Similarity-Based Method for Predicting Enzymatic Functions in Yeast Uncovers a New AMP Hydrolase. PMID:35123996
The properties of human disease mutations at protein interfaces. PMID:35120134
Systems pharmacology-based drug discovery and active mechanism of natural products for coronavirus pneumonia (COVID-19): An example using flavonoids. PMID:35114443
In vitro and in silico studies on clinically important enzymes inhibitory activities of flavonoids isolated from Euphorbia pulcherrima. PMID:35112936
p21-Activated Kinase 1 Promotes Breast Tumorigenesis via Phosphorylation and Activation of the Calcium/Calmodulin-Dependent Protein Kinase II. PMID:35111748
Accurate Prediction of Inhibitor Binding to HIV-1 Protease Using CANDOCK. PMID:35111726
Structure-based prediction of HDAC6 substrates validated by enzymatic assay reveals determinants of promiscuity and detects new potential substrates. PMID:35110592
Structure-guided stabilization of pathogen-derived peptide-HLA-E complexes using non-natural amino acids conserves native TCR recognition. PMID:35108401
GDP polyribonucleotidyltransferase domain of vesicular stomatitis virus polymerase regulates leader-promoter escape and polyadenylation-coupled termination during stop-start transcription. PMID:35108335
Highly Antiproliferative Latonduine and Indolo[2,3-c]quinoline Derivatives: Complex Formation with Copper(II) Markedly Changes the Kinase Inhibitory Profile. PMID:35104137
Most Probable Druggable Pockets in Mutant p53-Arg175His Clusters Extracted from Gaussian Accelerated Molecular Dynamics Simulations. PMID:35099676
ABlooper: Fast accurate antibody CDR loop structure prediction with accuracy estimation. PMID:35099535
Current structure predictors are not learning the physics of protein folding. PMID:35099504
Structure Determination of Microtubules and Pili: Past, Present, and Future Directions. PMID:35096976
From Acid Activation Mechanisms of Proton Conduction to Design of Inhibitors of the M2 Proton Channel of Influenza A Virus. PMID:35096969
Kinase Function of Brassinosteroid Receptor Specified by Two Allosterically Regulated Subdomains. PMID:35095975
Selective inhibition of nuclear export: a promising approach in the shifting treatment paradigms for hematological neoplasms. PMID:35091658
Trans-ancestral fine-mapping of MHC reveals key amino acids associated with spontaneous clearance of hepatitis C in HLA-DQβ1. PMID:35090584
Bioinformatics approaches identified dasatinib and bortezomib inhibit the activity of MCM7 protein as a potential treatment against human cancer. PMID:35087187
Statistical potentials from the Gaussian scaling behaviour of chain fragments buried within protein globules. PMID:35085247
Importin/exportin-mediated nucleocytoplasmic shuttling of cucumber mosaic virus 2b protein is required for 2b's efficient suppression of RNA silencing. PMID:35081172
Machine learning-driven identification of drugs inhibiting cytochrome P450 2C9. PMID:35081108
The structural coverage of the human proteome before and after AlphaFold. PMID:35073311
Benzoyl-xanthone derivative induces apoptosis in MCF-7 cells by binding TRAF6. PMID:35069862
Comparison between Heat-Clearing Medicine and Antirheumatic Medicine in Treatment of Gastric Cancer Based on Network Pharmacology, Molecular Docking, and Tumor Immune Infiltration Analysis. PMID:35069767
The Bacteroidetes Aequorivita sp. and Kaistella jeonii Produce Promiscuous Esterases With PET-Hydrolyzing Activity. PMID:35069509
Supercomputer simulation of the covalent inhibition of the main protease of SARS-CoV-2. PMID:35068913
Pharmacophore mapping of the crucial mediators of acetylcholinesterase and butyrylcholinesterase dual inhibition in Alzheimer's disease. PMID:35067751
A New Epitope Selection Method: Application to Design a Multi-Valent Epitope Vaccine Targeting HRAS Oncogene in Squamous Cell Carcinoma. PMID:35062725
Multi-Targeted Approaches and Drug Repurposing Reveal Possible SARS-CoV-2 Inhibitors. PMID:35062685
Simulation of Molecular Dynamics of SARS-CoV-2 S-Protein in the Presence of Multiple Arbidol Molecules: Interactions and Binding Mode Insights. PMID:35062323
Pan-cancer assessment of mutational landscape in intrinsically disordered hotspots reveals potential driver genes. PMID:35061901
Linking protein structural and functional change to mutation using amino acid networks. PMID:35061689
findMySequence: a neural-network-based approach for identification of unknown proteins in X-ray crystallography and cryo-EM. PMID:35059213
VfoldMCPX: predicting multistrand RNA complexes. PMID:35058350
Approach for the Design of Covalent Protein Kinase Inhibitors via Focused Deep Generative Modeling. PMID:35056884
Novel Molecular Targets of Antidepressants. PMID:35056845
Insulin Complexation with Cyclodextrins-A Molecular Modeling Approach. PMID:35056780
In Silico Prediction and Validation of CB2 Allosteric Binding Sites to Aid the Design of Allosteric Modulators. PMID:35056767
Study on Synergistic Antioxidant Effect of Typical Functional Components of Hydroethanolic Leaf Extract from Ginkgo Biloba In Vitro. PMID:35056751
Sequence and Structure-Based Analyses of Human Ankyrin Repeats. PMID:35056738
Quantum-Chemical Quasi-Docking for Molecular Dynamics Calculations. PMID:35055291
Biogenic Ferrihydrite Nanoparticles Produced by Klebsiella oxytoca: Characterization, Physicochemical Properties and Bovine Serum Albumin Interactions. PMID:35055266
CXCL1: Gene, Promoter, Regulation of Expression, mRNA Stability, Regulation of Activity in the Intercellular Space. PMID:35054978
Extracellular Calcium Receptor as a Target for Glutathione and Its Derivatives. PMID:35054903
Erythropoietin Interacts with Specific S100 Proteins. PMID:35053268
In Silico, In Vitro, and In Vivo Analysis of Tanshinone IIA and Cryptotanshinone from Salvia miltiorrhiza as Modulators of Cyclooxygenase-2/mPGES-1/Endothelial Prostaglandin EP3 Pathway. PMID:35053247
Molecular Determinants of Selectivity in Disordered Complexes May Shed Light on Specificity in Protein Condensates. PMID:35053240
Predicting Diagnostic Potential of Cathepsin in Epithelial Ovarian Cancer: A Design Validated by Computational, Biophysical and Electrochemical Data. PMID:35053201
Clustering of Aromatic Amino Acid Residues around Methionine in Proteins. PMID:35053154
In Silico Research of New Therapeutics Rotenoids Derivatives against Leishmania amazonensis Infection. PMID:35053132
Antimicrobial Activity of Snake β-Defensins and Derived Peptides. PMID:35050978
Computer-Aided Drug Design (CADD) to De-Orphanize Marine Molecules: Finding Potential Therapeutic Agents for Neurodegenerative and Cardiovascular Diseases. PMID:35049908
Spatio-temporal dynamics of intra-host variability in SARS-CoV-2 genomes. PMID:35048970
Proteome-scale mapping of binding sites in the unstructured regions of the human proteome. PMID:35044719
Selective Disruption of Survivin's Protein-Protein Interactions: A Supramolecular Approach Based on Guanidiniocarbonylpyrrole. PMID:35043526
Binding behavior of spike protein and receptor binding domain of the SARS-CoV-2 virus at different environmental conditions. PMID:35039570
A Thermodynamic Atlas of Proteomes Reveals Energetic Innovation across the Tree of Life. PMID:35038744
Methyl β-D-galactopyranoside esters as potential inhibitors for SARS-CoV-2 protease enzyme: synthesis, antimicrobial, PASS, molecular docking, molecular dynamics simulations and quantum computations. PMID:35037163
Structural Characterization of the Human Cytosolic Malate Dehydrogenase I. PMID:35036692
Structure-Based In Silico Investigation of Agonists for Proteins Involved in Breast Cancer. PMID:35035508
Multiple biological effects of secondary metabolites of Ziziphus jujuba: isolation and mechanistic insights through in vitro and in silico studies. PMID:35035286
Comparative genomic analysis of expansin superfamily gene members in zucchini and cucumber and their expression profiles under different abiotic stresses. PMID:35035133
Methyl β-D-galactopyranoside esters as potential inhibitors for SARS-CoV-2 protease enzyme: synthesis, antimicrobial, PASS, molecular docking, molecular dynamics simulations and quantum computations. PMID:35037163
Structural Characterization of the Human Cytosolic Malate Dehydrogenase I. PMID:35036692
Structure-Based In Silico Investigation of Agonists for Proteins Involved in Breast Cancer. PMID:35035508
Multiple biological effects of secondary metabolites of Ziziphus jujuba: isolation and mechanistic insights through in vitro and in silico studies. PMID:35035286
Comparative genomic analysis of expansin superfamily gene members in zucchini and cucumber and their expression profiles under different abiotic stresses. PMID:35035133
A naturally evolved mutation (Ser59Gly) in glutamine synthetase confers glufosinate resistance in plants. PMID:35029685
Simplified quality assessment for small-molecule ligands in the Protein Data Bank. PMID:35026162
Automated discovery of noncovalent inhibitors of SARS-CoV-2 main protease by consensus Deep Docking of 40 billion small molecules. PMID:35024120
The crystal structure of vaccinia virus protein E2 and perspectives on the prediction of novel viral protein folds. PMID:35020582
A Micrarchaeon Isolate Is Covered by a Proteinaceous S-Layer. PMID:35020453
Fragment Hotspot Mapping to Identify Selectivity-Determining Regions between Related Proteins. PMID:35020376
Current status of PTMs structural databases: applications, limitations and prospects. PMID:35020020
The N-terminal tail of the hydrophobin SC16 is not required for rodlet formation. PMID:35013607
Effective prediction of short hydrogen bonds in proteins via machine learning method. PMID:35013487
Helical structure motifs made searchable for functional peptide design. PMID:35013238
Co-Inhibition of P-gp and Hsp90 by an Isatin-Derived Compound Contributes to the Increase of the Chemosensitivity of MCF7/ADR-Resistant Cells to Doxorubicin. PMID:35011321
Synthesis, Molecular Docking and Biological Characterization of Pyrazine Linked 2-Aminobenzamides as New Class I Selective Histone Deacetylase (HDAC) Inhibitors with Anti-Leukemic Activity. PMID:35008795
Inhibition of the master regulator of Listeria monocytogenes virulence enables bacterial clearance from spacious replication vacuoles in infected macrophages. PMID:35007292
Cannabinoids Block Cellular Entry of SARS-CoV-2 and the Emerging Variants. PMID:35007072
Synthetic antibacterial discovery of symbah-1, a macrocyclic β-hairpin peptide antibiotic. PMID:35005555
A new glimpse on the active site of SARS-CoV-2 3CLpro, coupled with drug repurposing study. PMID:35001230
Comparison of PsbQ and Psb27 in photosystem II provides insight into their roles. PMID:35001227
Pharmacophore screening to identify natural origin compounds to target RNA-dependent RNA polymerase (RdRp) of SARS-CoV2. PMID:35000060
In silico design and in vitro assessment of anti-Helicobacter pylori compounds as potential small-molecule arginase inhibitors. PMID:34997872
A novel graph convolutional neural network for predicting interaction sites on protein kinase inhibitors in phosphorylation. PMID:34997142
Small, but powerful and attractive: 19F in biomolecular NMR. PMID:34995480
SAbDab in the age of biotherapeutics: updates including SAbDab-nano, the nanobody structure tracker. PMID:34986602
ONQUADRO: a database of experimentally determined quadruplex structures. PMID:34986600
Network pharmacology reveals the potential mechanism of Baiying Qinghou decoction in treating laryngeal squamous cell carcinoma. PMID:34986125
Backbone distortions in lactam-bridged helical peptides. PMID:34984761
A highly sensitive cell-based luciferase assay for high-throughput automated screening of SARS-CoV-2 nsp5/3CLpro inhibitors. PMID:34981051
The Nutritional Environment Is Sufficient To Select Coexisting Biofilm and Quorum Sensing Mutants of Pseudomonas aeruginosa. PMID:34978461
In silico Repurposing of Drugs for pan-HDAC and pan-SIRT Inhibitors: Consensus Structure-based Virtual Screening and Pharmacophore Modeling Investigations. PMID:34978402
Design, Synthesis, in vitro and in silico Characterization of 2-Quinolone-L-alaninate-1,2,3-triazoles as Antimicrobial Agents. PMID:34978160
Binding site identification of G protein-coupled receptors through a 3D Zernike polynomials-based method: application to C. elegans olfactory receptors. PMID:34977999
Accurate Machine Learning Prediction of Protein Circular Dichroism Spectra with Embedded Density Descriptors. PMID:34977905
Binding mode analysis of ABCA7 for the prediction of novel Alzheimer's disease therapeutics. PMID:34976306
Network Pharmacology and Molecular Docking Analyses of Mechanisms Underlying Effects of the Cyperi Rhizoma-Chuanxiong Rhizoma Herb Pair on Depression. PMID:34976096
Determination of tyrosinase-cyanidin-3-O-glucoside and (-/+)-catechin binding modes reveal mechanistic differences in tyrosinase inhibition. PMID:34969954
Embeddings from protein language models predict conservation and variant effects. PMID:34967936
Electrostatic Perturbations in the Substrate-Binding Pocket of Taurine/α-Ketoglutarate Dioxygenase Determine its Selectivity. PMID:34967481
A full-proteome, interaction-specific characterization of mutational hotspots across human cancers. PMID:34963661
In silico molecular docking and dynamic simulation of eugenol compounds against breast cancer. PMID:34962586
Mutagenic Distinction between the Receptor-Binding and Fusion Subunits of the SARS-CoV-2 Spike Glycoprotein and Its Upshot. PMID:34960255
Carissa macrocarpa Leaves Polar Fraction Ameliorates Doxorubicin-Induced Neurotoxicity in Rats via Downregulating the Oxidative Stress and Inflammatory Markers. PMID:34959705
A Deep-Learning Proteomic-Scale Approach for Drug Design. PMID:34959678
Understanding COVID-19 Pathogenesis: A Drug-Repurposing Effort to Disrupt Nsp-1 Binding to Export Machinery Receptor Complex. PMID:34959589
Low Blue Dose Photodynamic Therapy with Porphyrin-Iron Oxide Nanoparticles Complexes: In Vitro Study on Human Melanoma Cells. PMID:34959411
Characterizing fenestration size in sodium channel subtypes and their accessibility to inhibitors. PMID:34958776
Dipolar Order Parameters in Large Systems With Fast Spinning. PMID:34957221
Impact of Qi-Invigorating Traditional Chinese Medicines on Diffuse Large B Cell Lymphoma Based on Network Pharmacology and Experimental Validation. PMID:34955857
On the Dependence of Prion and Amyloid Structure on the Folding Environment. PMID:34948291
Origin of Increased Solvent Accessibility of Peptide Bonds in Mutual Synergetic Folding Proteins. PMID:34948202
Drug Discovery for Mycobacterium tuberculosis Using Structure-Based Computer-Aided Drug Design Approach. PMID:34948055
A Conserved Allosteric Site on Drug-Metabolizing CYPs: A Systematic Computational Assessment. PMID:34948012
Structural Insight into the Mechanism of PALB2 Interaction with MRG15. PMID:34946951
Selection of Promising Novel Fragment Sized S. aureus SrtA Noncovalent Inhibitors Based on QSAR and Docking Modeling Studies. PMID:34946760
DNA-Based Electrodes and Computational Approaches on the Intercalation Study of Antitumoral Drugs. PMID:34946705
Decoding the Structure of Non-Proteinogenic Amino Acids: The Rotational Spectrum of Jet-Cooled Laser-Ablated Thioproline. PMID:34946666
Monoterpene-Containing Substituted Coumarins as Inhibitors of Respiratory Syncytial Virus (RSV) Replication. PMID:34946573
Polyphenols as Potential Inhibitors of SARS-CoV-2 RNA Dependent RNA Polymerase (RdRp). PMID:34946521
Dissecting the Transcriptomes of Multiple Metronidazole-Resistant and Sensitive Trichomonas vaginalis Strains Identified Distinct Genes and Pathways Associated with Drug Resistance and Cell Death. PMID:34944632
Expression, Regulation, and Functions of the Galectin-16 Gene in Human Cells and Tissues. PMID:34944551
Three-Dimensional Graph Matching to Identify Secondary Structure Correspondence of Medium-Resolution Cryo-EM Density Maps. PMID:34944417
An Insight of RuBisCO Evolution through a Multilevel Approach. PMID:34944405
Inhibition of MurA Enzyme from Escherichia coli and Staphylococcus aureus by Diterpenes from Lepechinia meyenii and Their Synthetic Analogs. PMID:34943747
A longer isoform of Stim1 is a negative SOCE regulator but increases cAMP-modulated NFAT signaling. PMID:34942054
PreBINDS: An Interactive Web Tool to Create Appropriate Datasets for Predicting Compound-Protein Interactions. PMID:34938773
Systematized analysis of secondary structure dependence of key structural features of residues in soluble and membrane-bound proteins. PMID:34934943
Sdfconf: A Novel, Flexible, and Robust Molecular Data Management Tool. PMID:34932340
Predicting Protein-Peptide Complex Structures by Accounting for Peptide Flexibility and the Physicochemical Environment. PMID:34931833
Characterization of the AGR2 Interactome Uncovers New Players of Protein Disulfide Isomerase Network in Cancer Cells. PMID:34929376
Thioesterase enzyme families: Functions, structures, and mechanisms. PMID:34921469
Analysing an allelic series of rare missense variants of CACNA1I in a Swedish schizophrenia cohort. PMID:34919654
Inactive-to-Active Transition of Human Thymidine Kinase 1 Revealed by Molecular Dynamics Simulations. PMID:34919400
Allosteric regulation of binding specificity of HVEM for CD160 and BTLA ligands upon G89F mutation. PMID:34917954
In silico evaluation of naturally isolated triterpene glycosides (TG) from Gymnema sylvestre towards diabetic treatment. PMID:34917786
Mutations in LRRK2 linked to Parkinson disease sequester Rab8a to damaged lysosomes and regulate transferrin-mediated iron uptake in microglia. PMID:34914695
EpiCurator: an immunoinformatic workflow to predict and prioritize SARS-CoV-2 epitopes. PMID:34909278
Worldwide Protein Data Bank (wwPDB): A virtual treasure for research in biotechnology. PMID:34908533
Proteomics advances towards developing SARS-CoV-2 therapeutics using in silico drug repurposing approaches. PMID:34906319
SSBP1-Disease Update: Expanding the Genetic and Clinical Spectrum, Reporting Variable Penetrance and Confirming Recessive Inheritance. PMID:34905022
In Silico Elucidation of Potent Inhibitors and Rational Drug Design against SARS-CoV-2 Papain-like Protease. PMID:34904832
T-cell epitope-based vaccine designing against Orthohantavirus: a causative agent of deadly cardio-pulmonary disease. PMID:34900515
MUfoldQA_G: High-accuracy protein model QA via retraining and transformation. PMID:34900138
Benchmarking the Performance of Irregular Computations in AutoDock-GPU Molecular Docking. PMID:34898769
2-Aminobenzoxazole-appended coumarins as potent and selective inhibitors of tumour-associated carbonic anhydrases. PMID:34894971
Structure-based virtual screening and biological evaluation of novel small-molecule BTK inhibitors. PMID:34894949
DeepVASP-E: A Flexible Analysis of Electrostatic Isopotentials for Finding and Explaining Mechanisms that Control Binding Specificity. PMID:34890136
Transferability of Geometric Patterns from Protein Self-Interactions to Protein-Ligand Interactions. PMID:34890133
Computational Construction of a Single-Chain Bi-Paratopic Antibody Allosterically Inhibiting TCR-Staphylococcal Enterotoxin B Binding. PMID:34887850
Transcriptomics Changes in the Peritoneum of Mice with Lipopolysaccharide-Induced Peritonitis. PMID:34884814
Exploiting Structural Modelling Tools to Explore Host-Translocated Effector Proteins. PMID:34884778
Homodimeric and Heterodimeric Interactions among Vertebrate Basic Helix-Loop-Helix Transcription Factors. PMID:34884664
Synthesis, In Vitro and In Silico Anticancer Activity of New 4-Methylbenzamide Derivatives Containing 2,6-Substituted Purines as Potential Protein Kinases Inhibitors. PMID:34884546
Rare Glutamic Acid Methyl Ester Peptaibols from Sepedonium ampullosporum Damon KSH 534 Exhibit Promising Antifungal and Anticancer Activity. PMID:34884518
Mutations That Affect the Surface Expression of TRPV6 Are Associated with the Upregulation of Serine Proteases in the Placenta of an Infant. PMID:34884497
Characteration of a novel arylesterase from probiotics Lacticaseibacillus rhamnosus GG with the preference for medium- and long-chain p-Nitrophenyl esters. PMID:34881159
Design of a methotrexate-controlled chemical dimerization system and its use in bio-electronic devices. PMID:34880210
Design principles that protect the proteasome from self-destruction. PMID:34878680
Nonstandard RNA/RNA interactions likely enhance folding and stability of segmented ribosomes. PMID:34876487
IMGT® databases, related tools and web resources through three main axes of research and development. PMID:34875068
Exploration of Dark Chemical Genomics Space via Portal Learning: Applied to Targeting the Undruggable Genome and COVID-19 Anti-Infective Polypharmacology. PMID:34873596
CoCoNet-boosting RNA contact prediction by convolutional neural networks. PMID:34871451
Potential inhibitors of SARS-CoV-2 (COVID 19) proteases PLpro and Mpro/ 3CLpro: molecular docking and simulation studies of three pertinent medicinal plant natural components. PMID:34870149
Systematic review on role of structure based drug design (SBDD) in the identification of anti-viral leads against SARS-Cov-2. PMID:34870145
Designing of a Multi-epitope Vaccine against the Structural Proteins of Marburg Virus Exploiting the Immunoinformatics Approach. PMID:34870027
The impact of folding modes and deuteration on the atomic resolution structure of hen egg-white lysozyme. PMID:34866613
Structure of mitogen-activated protein kinase kinase 1 in the DFG-out conformation. PMID:34866601
GLYCO: a tool to quantify glycan shielding of glycosylated proteins. PMID:34864901
DeepRank: a deep learning framework for data mining 3D protein-protein interfaces. PMID:34862392
Author-sourced capture of pathway knowledge in computable form using Biofactoid. PMID:34860157
Structure-based deep learning for binding site detection in nucleic acid macromolecules. PMID:34859211
Multiscale interactome analysis coupled with off-target drug predictions reveals drug repurposing candidates for human coronavirus disease. PMID:34857794
Functional enrichment of alternative splicing events with NEASE reveals insights into tissue identity and diseases. PMID:34857024
A Conformationally Stable Acyclic β-Hairpin Scaffold Tolerating the Incorporation of Poorly β-Sheet-Prone Amino Acids. PMID:34856053
SCOPe: improvements to the structural classification of proteins - extended database to facilitate variant interpretation and machine learning. PMID:34850923
Binder design for targeting SARS-CoV-2 spike protein: An in silico perspective. PMID:34849425
Anti-breast cancer synthetic peptides derived from the Anabas testudineus skin mucus fractions. PMID:34848729
Predicting the Structure of a Viroid : Structure, Structure Distribution, Consensus Structure, and Structure Drawing. PMID:34845705
A 3D structural SARS-CoV-2-human interactome to explore genetic and drug perturbations. PMID:34845387
The CRISPR-associated Cas4 protein from Leptospira interrogans demonstrate versatile nuclease activity. PMID:34841331
Fermentation optimization of cellulase production from sugarcane bagasse by Bacillus pseudomycoides and molecular modeling study of cellulase. PMID:34841306
Polyethylenimine-Poly(lactic-co-glycolic acid)2 Nanoparticles Show an Innate Targeting Ability to the Submandibular Salivary Gland via the Muscarinic 3 Receptor. PMID:34841064
Molecular modeling piloted analysis for semicarbazone derivative of curcumin as a potent Abl-kinase inhibitor targeting colon cancer. PMID:34840927
Experimental evolution of the megaplasmid pMPPla107 in Pseudomonas stutzeri enables identification of genes contributing to sensitivity to an inhibitory agent. PMID:34839711
Phylogenetic Characteristics of Canine Parvovirus Type 2c Variant Endemic in Shanghai, China. PMID:34835063
Molecular Docking and Virtual Screening of an Influenza Virus Inhibitor That Disrupts Protein-Protein Interactions. PMID:34835035
Mutational Hotspot in the SARS-CoV-2 Spike Protein N-Terminal Domain Conferring Immune Escape Potential. PMID:34834921
The Antileukemic Effect of Xestoquinone, A Marine-Derived Polycyclic Quinone-Type Metabolite, Is Mediated through ROS-Induced Inhibition of HSP-90. PMID:34834129
Synthesis, Antimicrobial, Anticancer, PASS, Molecular Docking, Molecular Dynamic Simulations & Pharmacokinetic Predictions of Some Methyl β-D-Galactopyranoside Analogs. PMID:34834107
Discovery of New Ginsenol-Like Compounds with High Antiviral Activity. PMID:34833886
Investigation of Thiocarbamates as Potential Inhibitors of the SARS-CoV-2 Mpro. PMID:34832935
Inhibition of XPO-1 Mediated Nuclear Export through the Michael-Acceptor Character of Chalcones. PMID:34832913
Three-Component Synthesis of 2-Amino-3-cyano-4H-chromenes, In Silico Analysis of Their Pharmacological Profile, and In Vitro Anticancer and Antifungal Testing. PMID:34832892
Biogenic Synthesis and Characterization of Antioxidant and Antimicrobial Silver Nanoparticles Using Flower Extract of Couroupita guianensis Aubl. PMID:34832255
New Investigations with Lupane Type A-Ring Azepane Triterpenoids for Antimycobacterial Drug Candidate Design. PMID:34830423
Dissimilar Ligands Bind in a Similar Fashion: A Guide to Ligand Binding-Mode Prediction with Application to CELPP Studies. PMID:34830201
Purification, Identification and Characterization of Antioxidant Peptides from Corn Silk Tryptic Hydrolysate: An Integrated In Vitro-In Silico Approach. PMID:34829693
Computational Insights into the Binding Mechanism of OxyS sRNA with Chaperone Protein Hfq. PMID:34827651
Bioinformatic Analysis of Lytic Polysaccharide Monooxygenases Reveals the Pan-Families Occurrence of Intrinsically Disordered C-Terminal Extensions. PMID:34827630
Improving Protein Subcellular Location Classification by Incorporating Three-Dimensional Structure Information. PMID:34827605
Bayesian probabilistic assignment of chemical shifts in organic solids. PMID:34826232
Target identification for repurposed drugs active against SARS-CoV-2 via high-throughput inverse docking. PMID:34825285
Engineering a PAM-flexible SpdCas9 variant as a universal gene repressor. PMID:34824292
Carbon fullerene and nanotube are probable binders to multiple targets of SARS-CoV-2: Insights from computational modeling and molecular dynamic simulation studies. PMID:34823028
In Silico Analysis of Glucose Oxidase from Aspergillus niger: Potential Cysteine Mutation Sites for Enhancing Protein Stability. PMID:34821754
A roadmap for metagenomic enzyme discovery. PMID:34821235
Evaluation of the stereochemical quality of predicted RNA 3D models in the RNA-Puzzles submissions. PMID:34819324
Antinociceptive and anti-inflammatory effects of hydrazone derivatives and their possible mechanism of action in mice. PMID:34818331
Fundamental Tick Vaccinomic Approach to Evade Host Autoimmune Reaction. PMID:34816415
Unexpected similarity between HIV-1 reverse transcriptase and tumor necrosis factor binding sites revealed by computer vision. PMID:34814950
Slowest-first protein translation scheme: Structural asymmetry and co-translational folding. PMID:34813729
Rational-Design Engineering to Improve Enzyme Thermostability. PMID:34813064
Intergenic ORFs as elementary structural modules of de novo gene birth and protein evolution. PMID:34810219
A network pharmacology approach to reveal the pharmacological targets and biological mechanism of compound kushen injection for treating pancreatic cancer based on WGCNA and in vitro experiment validation. PMID:34809653
Impact of Deleterious Mutations on Structure, Function and Stability of Serum/Glucocorticoid Regulated Kinase 1: A Gene to Diseases Correlation. PMID:34805284
In vitro and molecular docking and analysis of isoxazoline derivatives with DPPH. PMID:34803253
Mechanistic insights into the renoprotective role of curcumin in cisplatin-induced acute kidney injury: network pharmacology analysis and experimental validation. PMID:34802380
Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. PMID:34801754
PremPLI: a machine learning model for predicting the effects of missense mutations on protein-ligand interactions. PMID:34799678
Expression level is a major modifier of the fitness landscape of a protein coding gene. PMID:34795386
Revealing A-T and G-C Hoogsteen base pairs in stressed protein-bound duplex DNA. PMID:34792150
Zn-Induced Interactions Between SARS-CoV-2 orf7a and BST2/Tetherin. PMID:34791819
proChIPdb: a chromatin immunoprecipitation database for prokaryotic organisms. PMID:34791440
FuzDB: a new phase in understanding fuzzy interactions. PMID:34791357
CellPAINT: Turnkey Illustration of Molecular Cell Biology. PMID:34790910
Targeting the Central Pocket of the Pseudomonas aeruginosa Lectin LecA. PMID:34788491
Undervalued Pseudo-nifH Sequences in Public Databases Distort Metagenomic Insights into Biological Nitrogen Fixers. PMID:34787447
Strategies to identify candidate repurposable drugs: COVID-19 treatment as a case example. PMID:34785660
Optimal structure determination from sub-optimal diffraction data. PMID:34783106
Interaction of Spike protein and lipid membrane of SARS-CoV-2 with Ursodeoxycholic acid, an in-silico analysis. PMID:34782703
ZHX2 promotes HIF1α oncogenic signaling in triple-negative breast cancer. PMID:34779768
Tailored Parameterization of the LIE Method for Calculating the Binding Free Energy of Vps34-Inhibitor Complexes. PMID:34778624
One-Pot Surface Modification of β-Cu2O NPs for Biocatalytic Performance against A-549 Lung Carcinoma Cell Lines through Docking Analysis. PMID:34778611
Structural and functional significance of the amino acid differences Val35Thr, Ser46Ala, Asn65Ser, and Ala94Ser in 3C-like proteinases from SARS-CoV-2 and SARS-CoV. PMID:34774600
New Therapeutic Strategy for Overcoming Multidrug Resistance in Cancer Cells with Pyrazolo[3,4-d]pyrimidine Tyrosine Kinase Inhibitors. PMID:34771471
Tepotinib Inhibits Several Drug Efflux Transporters and Biotransformation Enzymes: The Role in Drug-Drug Interactions and Targeting Cytostatic Resistance In Vitro and Ex Vivo. PMID:34769363
Structural and Functional Characterization of One Unclassified Glutathione S-Transferase in Xenobiotic Adaptation of Leptinotarsa decemlineata. PMID:34769352
Ensemble of Template-Free and Template-Based Classifiers for Protein Secondary Structure Prediction. PMID:34768880
Analysis of L-DOPA and droxidopa binding to human β2-adrenergic receptor. PMID:34767786
Genetic diversity, antifungal evaluation and molecular docking studies of Cu-chitosan nanoparticles as prospective stem rust inhibitor candidates among some Egyptian wheat genotypes. PMID:34767570
DeepREx-WS: A web server for characterising protein-solvent interaction starting from sequence. PMID:34765094
A Deep Learning and XGBoost-Based Method for Predicting Protein-Protein Interaction Sites. PMID:34764983
Toward a Computational NMR Procedure for Modeling Dipeptide Side-Chain Conformation. PMID:34762416
SAXSMoW 3.0: New advances in the determination of the molecular weight of proteins in dilute solutions from SAXS intensity data on a relative scale. PMID:34761467
SCoV2-MD: a database for the dynamics of the SARS-CoV-2 proteome and variant impact predictions. PMID:34761257
Cytotoxic and Antifungal Amides Derived from Ferulic Acid: Molecular Docking and Mechanism of Action. PMID:34761004
The trRosetta server for fast and accurate protein structure prediction. PMID:34759384
CHARMM-GUI Ligand Designer for Template-Based Virtual Ligand Design in a Binding Site. PMID:34757752
Extended antibody-framework-to-antigen distance observed exclusively with broad HIV-1-neutralizing antibodies recognizing glycan-dense surfaces. PMID:34753907
Purinergic GPCR transmembrane residues involved in ligand recognition and dimerization. PMID:34752329
INDI-integrated nanobody database for immunoinformatics. PMID:34747487
Nanobase.org: a repository for DNA and RNA nanostructures. PMID:34747480
Allosteric pockets and dynamic residue network hubs of falcipain 2 in mutations including those linked to artemisinin resistance. PMID:34745456
RCSB Protein Data Bank resources for structure-facilitated design of mRNA vaccines for existing and emerging viral pathogens. PMID:34739839
RNALigands: a database and web server for RNA-ligand interactions. PMID:34732566
Deep Learning in Structure-Based Drug Design. PMID:34731473
Deep Learning and Computational Chemistry. PMID:34731467
MCDB: A comprehensive curated mitotic catastrophe database for retrieval, protein sequence alignment, and target prediction. PMID:34729303
Synthesis, cytotoxicity and docking studies (with SARS-CoV-2) of water-soluble binuclear Ru-p-cymene complex holding indole thiosemicarbazone ligand. PMID:34729032
Pharmacoinformatics-based investigation of bioactive compounds of Rasam (South Indian recipe) against human cancer. PMID:34728718
Cryo-EM structures of PI3Kα reveal conformational changes during inhibition and activation. PMID:34725156
An automated platform for structural analysis of membrane proteins through serial crystallography. PMID:34723237
Improved Protein Structure Prediction Using a New Multi-Scale Network and Homologous Templates. PMID:34719864
Functional Annotation from Structural Homology. PMID:34718998
The Eukaryotic Linear Motif resource: 2022 release. PMID:34718738
VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center. PMID:34718728
Transcriptomic analysis of Rhodococcus opacus R7 grown on polyethylene by RNA-seq. PMID:34716360
Epitope-imprinted polymers: Design principles of synthetic binding partners for natural biomacromolecules. PMID:34714673
Dinuclear platinum(II) complexes as the pattern for phosphate backbone binding: a new perspective for recognition of binding modes to DNA. PMID:34714401
Why are large conformational changes well described by harmonic normal modes? PMID:34710378
Beta turn propensity and a model polymer scaling exponent identify intrinsically disordered phase-separating proteins. PMID:34710373
Structural and functional analysis of somatic coding and UTR indels in breast and lung cancer genomes. PMID:34707120
Antarctic Polyester Hydrolases Degrade Aliphatic and Aromatic Polyesters at Moderate Temperatures. PMID:34705547
Accurate prediction of protein torsion angles using evolutionary signatures and recurrent neural network. PMID:34702851
Parakeet: a digital twin software pipeline to assess the impact of experimental parameters on tomographic reconstructions for cryo-electron tomography. PMID:34699732
Molecular Basis of Ca(II)-Induced Tetramerization and Transition-Metal Sequestration in Human Calprotectin. PMID:34699194
Stacked but not Stuck: Unveiling the Role of π→π* Interactions with the Help of the Benzofuran-Formaldehyde Complex. PMID:34697878
Antibody elicited by HIV-1 immunogen vaccination in macaques displaces Env fusion peptide and destroys a neutralizing epitope. PMID:34697307
In Silico Structure-Based Design of Antiviral Peptides Targeting the Severe Fever with Thrombocytopenia Syndrome Virus Glycoprotein Gn. PMID:34696477
Synergistic Effects of Natural Compounds Toward Inhibition of SARS-CoV-2 3CL Protease. PMID:34694807
Borcalein: a Carborane-Based Analogue of Baicalein with 12-Lipoxygenase-Independent Toxicity. PMID:34694057
Se⋅⋅⋅O/S and S⋅⋅⋅O Chalcogen Bonds in Small Molecules and Proteins: A Combined CSD and PDB Study. PMID:34693623
Inhibition Potencies of Phytochemicals Derived from Sesame Against SARS-CoV-2 Main Protease: A Molecular Docking and Simulation Study. PMID:34692642
Disassembly of microtubules by intense terahertz pulses. PMID:34692217
Identification of Novel Potential VEGFR-2 Inhibitors Using a Combination of Computational Methods for Drug Discovery. PMID:34685441
In Silico and In Vivo Evaluation of SARS-CoV-2 Predicted Epitopes-Based Candidate Vaccine. PMID:34684763
In Silico Identification of Possible Inhibitors for Protein Kinase B (PknB) of Mycobacterium tuberculosis. PMID:34684743
In Vitro Anti-Tubulin Activity on MCF10A Cell Line and In Silico Rigid/Semiflexible-Residues Docking, of Two Lignans from Bursera Fagaroides var. Fagaroides. PMID:34684736
Emerging Mutations in Nsp1 of SARS-CoV-2 and Their Effect on the Structural Stability. PMID:34684233
Functionalizing Ferritin Nanoparticles for Vaccine Development. PMID:34683914
Identification of Effective Anticancer G-Quadruplex-Targeting Chemotypes through the Exploration of a High Diversity Library of Natural Compounds. PMID:34683905
Structural Insight into a Yeast Maltase-The BaAG2 from Blastobotrys adeninivorans with Transglycosylating Activity. PMID:34682239
Screening of β1- and β2-Adrenergic Receptor Modulators through Advanced Pharmacoinformatics and Machine Learning Approaches. PMID:34681845
MAP/Microtubule Affinity Regulating Kinase 4 Inhibitory Potential of Irisin: A New Therapeutic Strategy to Combat Cancer and Alzheimer's Disease. PMID:34681645
Novel Synthesized N-Ethyl-Piperazinyl-Amides of C2-Substituted Oleanonic and Ursonic Acids Exhibit Cytotoxic Effects through Apoptotic Cell Death Regulation. PMID:34681629
In Silico Studies of Potential Selective Inhibitors of Thymidylate Kinase from Variola virus. PMID:34681251
In Silico Prediction of the Phosphorylation of NS3 as an Essential Mechanism for Dengue Virus Replication and the Antiviral Activity of Quercetin. PMID:34681164
NBD2 Is Required for the Rescue of Mutant F508del CFTR by a Thiazole-Based Molecule: A Class II Corrector for the Multi-Drug Therapy of Cystic Fibrosis. PMID:34680050
A Novel Sesquiterpene Lactone Xanthatin-13-(pyrrolidine-2-carboxylic acid) Isolated from Burdock Leaf Up-Regulates Cells' Oxidative Stress Defense Pathway. PMID:34679753
LC-MS Based Analysis and Biological Properties of Pseudocedrela kotschyi (Schweinf.) Harms Extracts: A Valuable Source of Antioxidant, Antifungal, and Antibacterial Compounds. PMID:34679706
Changes in Protein Structural Motifs upon Post-Translational Modification in Kidney Cancer. PMID:34679534
Investigating single amino acid substitutions in PIM1 kinase: A structural genomics approach. PMID:34679086
Contemporary Approaches to the Discovery and Development of Broad-Spectrum Natural Product Prototypes for the Control of Coronaviruses. PMID:34677966
RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D. PMID:34676613
The V2475F CPVT1 mutation yields distinct RyR2 channel populations that differ in their responses to cytosolic Ca2+ and Mg2. PMID:34676560
Performance Assessment of the Network Reconstruction Approaches on Various Interactomes. PMID:34676243
Comprehensive discovery of CRISPR-targeted terminally redundant sequences in the human gut metagenome: Viruses, plasmids, and more. PMID:34673779
Molecular dynamics: a powerful tool for studying the medicinal chemistry of ion channel modulators. PMID:34671734
Structure-guided machine learning prediction of drug resistance mutations in Abelson 1 kinase. PMID:34667533
Structural and Biochemical Characterization of Cysteinylation in Broadly Neutralizing Antibodies to HIV-1. PMID:34666044
Graph representation learning for structural proteomics. PMID:34665257
RR3DD: an RNA global structure-based RNA three-dimensional structural classification database. PMID:34663179
Conformational variability of loops in the SARS-CoV-2 spike protein. PMID:34661307
A Probabilistic Programming Approach to Protein Structure Superposition. PMID:34661202
Atomistic Simulations and In Silico Mutational Profiling of Protein Stability and Binding in the SARS-CoV-2 Spike Protein Complexes with Nanobodies: Molecular Determinants of Mutational Escape Mechanisms. PMID:34660995
Search for RNA aptamers against non-structural protein of SARS-CoV-2: Design using molecular dynamics approach. PMID:34660818
Borinostats: solid-phase synthesis of carborane-capped histone deacetylase inhibitors with a tailor-made selectivity profile. PMID:34659728
Genetic and Phenotypic Characterization of the Novel Metallo-β-Lactamase NDM-29 From Escherichia coli. PMID:34659178
The impact of cross-docked poses on performance of machine learning classifier for protein-ligand binding pose prediction. PMID:34656169
Discovery of inhibitors targeting protein tyrosine phosphatase 1B using a combined virtual screening approach. PMID:34655403
Long-term stability predictions of therapeutic monoclonal antibodies in solution using Arrhenius-based kinetics. PMID:34654882
Improving Structure-Based Virtual Screening with Ensemble Docking and Machine Learning. PMID:34652141
Application of Computational Methods in Understanding Mutations in Mycobacterium tuberculosis Drug Resistance. PMID:34651013
SMART v1.0: A Database for Small Molecules with Functional Implications in Plants. PMID:34648133
NCATS Inxight Drugs: a comprehensive and curated portal for translational research. PMID:34648031
DFT calculations to investigate silver ions as a virucide from SARS-CoV-2. PMID:34643800
Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. PMID:34642465
FoldHSphere: deep hyperspherical embeddings for protein fold recognition. PMID:34641786
Design, Synthesis, Biological Evaluation and In Silico Study of Benzyloxybenzaldehyde Derivatives as Selective ALDH1A3 Inhibitors. PMID:34641313
Interaction of Thymine DNA Glycosylase with Oxidised 5-Methyl-cytosines in Their Amino- and Imino-Forms. PMID:34641273
Pathogenesis of IgA Nephropathy: Current Understanding and Implications for Development of Disease-Specific Treatment. PMID:34640530
Loops around the Heme Pocket Have a Critical Role in the Function and Stability of BsDyP from Bacillus subtilis. PMID:34639208
Molecular Mechanism of the Anti-Inflammatory Action of Heparin. PMID:34639073
3-Pyridinylidene Derivatives of Chemically Modified Lupane and Ursane Triterpenes as Promising Anticancer Agents by Targeting Apoptosis. PMID:34639035
Esterase Activity of Serum Albumin Studied by 1H NMR Spectroscopy and Molecular Modelling. PMID:34638934
Low-Frequency Harmonic Perturbations Drive Protein Conformational Changes. PMID:34638837
Design, Synthesis and Anticancer Profile of New 4-(1H-benzo[d]imidazol-1-yl)pyrimidin-2-amine-Linked Sulfonamide Derivatives with V600EBRAF Inhibitory Effect. PMID:34638829
Synthesis and In Silico Docking of New Pyrazolo[4,3-e]pyrido[1,2-a]pyrimidine-based Cytotoxic Agents. PMID:34638600
Mass Spectrometric and Bio-Computational Binding Strength Analysis of Multiply Charged RNAse S Gas-Phase Complexes Obtained by Electrospray Ionization from Varying In-Solution Equilibrium Conditions. PMID:34638522
Consensus Virtual Screening Identified [1,2,4]Triazolo[1,5-b]isoquinolines As MELK Inhibitor Chemotypes. PMID:34632716
Interpretable artificial intelligence and exascale molecular dynamics simulations to reveal kinetics: Applications to Alzheimer's disease. PMID:34628220
Molecular docking analysis of Plasmodium falciparum dihydroorotate dehydrogenase towards the design of effective inhibitors. PMID:34621112
Effect of drug metabolism in the treatment of SARS-CoV-2 from an entirely computational perspective. PMID:34620963
Molecular insight into the affinity, specificity and cross-reactivity of systematic hepatocellular carcinoma RALT interaction profile with human receptor tyrosine kinases. PMID:34618235
Exploring the mechanism of Jianpi Qushi Huayu Formula in the treatment of chronic glomerulonephritis based on network pharmacology. PMID:34618179
Accurate Prediction of Hydration Sites of Proteins Using Energy Model With Atom Embedding. PMID:34616774
SAS: A Platform of Spike Antigenicity for SARS-CoV-2. PMID:34616728
Intrinsically disordered proteins: modes of binding with emphasis on disordered domains. PMID:34610267
Vanillin enones as selective inhibitors of the cancer associated carbonic anhydrase isoforms IX and XII. The out of the active site pocket for the design of selective inhibitors? PMID:34607524
Hypervariability of accessible and inaccessible conformational space of proteins. PMID:34604793
Targeting cathepsins: A potential link between COVID-19 and associated neurological manifestations. PMID:34604555
PDB-101: Educational resources supporting molecular explorations through biology and medicine. PMID:34601771
DisCovER: distance- and orientation-based covariational threading for weakly homologous proteins. PMID:34599831
Unique features of different classes of G-protein-coupled receptors revealed from sequence coevolutionary and structural analysis. PMID:34599827
Molecular and genetic characterization of a large Brazilian cohort presenting hearing loss. PMID:34599368
Molecular Modeling and Bioinformatics Analysis of Drug-Receptor Interactions in the System Formed by Glargine, Its Metabolite M1, the Insulin Receptor, and the IGF1 Receptor. PMID:34594103
COVIDrugNet: a network-based web tool to investigate the drugs currently in clinical trial to contrast COVID-19. PMID:34593915
High throughput and quantitative enzymology in the genomic era. PMID:34592682
In silico characterization of the GH5-cellulase family from uncultured microorganisms: physicochemical and structural studies. PMID:34591195
Proteomic and molecular dynamic investigations of PTM-induced structural fluctuations in breast and ovarian cancer. PMID:34588485
Computational prediction of the effect of amino acid changes on the binding affinity between SARS-CoV-2 spike RBD and human ACE2. PMID:34588290
Importance of Anion-π Interactions in RNA GAAA and GGAG Tetraloops: A Combined MD and QM Study. PMID:34586810
AlphaMap: an open-source python package for the visual annotation of proteomics data with sequence specific knowledge. PMID:34586352
Decline of protein structure rigidity with interatomic distance. PMID:34583630
CPLM 4.0: an updated database with rich annotations for protein lysine modifications. PMID:34581824
CovPDB: a high-resolution coverage of the covalent protein-ligand interactome. PMID:34581813
The pockets guide to HLA class I molecules. PMID:34581761
Evolution of the SARS-CoV-2 proteome in three dimensions (3D) during the first 6 months of the COVID-19 pandemic. PMID:34580920
Evaluation of Inhibitory Activity In Silico of In-House Thiomorpholine Compounds between the ACE2 Receptor and S1 Subunit of SARS-CoV-2 Spike. PMID:34578240
pH-Dependent Structural Dynamics of Cathepsin D-Family Aspartic Peptidase of Clonorchis sinensis. PMID:34578162
In Silico-Based Design and In Vivo Evaluation of an Anthranilic Acid Derivative as a Multitarget Drug in a Diet-Induced Metabolic Syndrome Model. PMID:34577613
Semaphorin 3A-Glycosaminoglycans Interaction as Therapeutic Target for Axonal Regeneration. PMID:34577606
Polyphenols from Citrus Tacle® Extract Endowed with HMGCR Inhibitory Activity: An Antihypercholesterolemia Natural Remedy. PMID:34577189
In Silico Analysis of Fungal and Chloride-Dependent α-Amylases within the Family GH13 with Identification of Possible Secondary Surface-Binding Sites. PMID:34577174
Controlling the Substrate Specificity of an Enzyme through Structural Flexibility by Varying the Salt-Bridge Density. PMID:34577164
Interaction of (+)-Strebloside and Its Derivatives with Na+/K+-ATPase and Other Targets. PMID:34577146
Exploring the Role of L10 Loop in New Delhi Metallo-β-lactamase (NDM-1): Kinetic and Dynamic Studies. PMID:34576958
Conformational Insights into the Control of CNF1 Toxin Activity by Peptidyl-Prolyl Isomerization: A Molecular Dynamics Perspective. PMID:34576292
Insights into Comparative Modeling of VHH Domains. PMID:34575931
Inhibition of UBA5 Expression and Induction of Autophagy in Breast Cancer Cells by Usenamine A. PMID:34572561
Revealing the Mutation Patterns of Drug-Resistant Reverse Transcriptase Variants of Human Immunodeficiency Virus through Proteochemometric Modeling. PMID:34572515
Comparative Genomic Analysis of the DUF34 Protein Family Suggests Role as a Metal Ion Chaperone or Insertase. PMID:34572495
Towards Understanding the Pathogenicity of DROSHA Mutations in Oncohematology. PMID:34572006
Comparative analysis of the unbinding pathways of antiviral drug Indinavir from HIV and HTLV1 proteases by supervised molecular dynamics simulation. PMID:34570822
On the use of intra-molecular distance and angle constraints to lengthen the time step in molecular and stochastic dynamics simulations of proteins. PMID:34569110
Phylogenetic Comparison and Splicing Analysis of the U1 snRNP-specific Protein U1C in Eukaryotes. PMID:34568424
Polyphenols as alternative treatments of COVID-19. PMID:34567475
RSK1 vs. RSK2 Inhibitory Activity of the Marine β-Carboline Alkaloid Manzamine A: A Biochemical, Cervical Cancer Protein Expression, and Computational Study. PMID:34564169
Features and futures of X-ray free-electron lasers. PMID:34557749
dockECR: Open consensus docking and ranking protocol for virtual screening of small molecules. PMID:34555725
Path to improving the life cycle and quality of genome-scale models of metabolism. PMID:34555324
Writing a strong scientific paper in medicine and the biomedical sciences: a checklist and recommendations for early career researchers. PMID:34554491
ZoomQA: residue-level protein model accuracy estimation with machine learning on sequential and 3D structural features. PMID:34553747
PncsHub: a platform for annotating and analyzing non-classically secreted proteins in Gram-positive bacteria. PMID:34551435
Bio-informatics and in Vitro Experiments Reveal the Mechanism of Schisandrin A Against MDA-MB-231 cells. PMID:34550868
DLAB-Deep learning methods for structure-based virtual screening of antibodies. PMID:34546288
INK4 Tumor Suppressor Proteins Mediate Resistance to CDK4/6 Kinase Inhibitors. PMID:34544752
Proteomic Tools for the Analysis of Cytoskeleton Proteins. PMID:34542864
Cycloastragenol alleviates airway inflammation in asthmatic mice by inhibiting autophagy. PMID:34542166
Investigation of structural analogs of hydroxychloroquine for SARS-CoV-2 main protease (Mpro): A computational drug discovery study. PMID:34537554
The molecular mechanism of phytosphingosine binding to FFAR4/GPR120 differs from that of other fatty acids. PMID:34535977
A method for intuitively extracting macromolecular dynamics from structural disorder. PMID:34535675
Hepatic Regulator of G Protein Signaling 6 (RGS6) drives non-alcoholic fatty liver disease by promoting oxidative stress and ATM-dependent cell death. PMID:34534913
Indomethacin-based PROTACs as pan-coronavirus antiviral agents. PMID:34534839
Network pharmacology study on the mechanism of Qiangzhifang in the treatment of panic disorder. PMID:34532487
Interpreting a black box predictor to gain insights into early folding mechanisms. PMID:34527196
The search for molecular mimicry in proteins carried by extracellular vesicles secreted by cells infected with Plasmodium falciparum. PMID:34527168
A deep-learning framework for multi-level peptide-protein interaction prediction. PMID:34526500
Principal component analysis of alpha-helix deformations in transmembrane proteins. PMID:34525125
Natural Occurring Polymorphisms in HIV-1 Integrase and RNase H Regulate Viral Release and Autoprocessing. PMID:34523971
PDB-wide identification of physiological hetero-oligomeric assemblies based on conserved quaternary structure geometry. PMID:34520740
SARS-CoV-2 structural coverage map reveals viral protein assembly, mimicry, and hijacking mechanisms. PMID:34519429
Rare genetic variability in human drug target genes modulates drug response and can guide precision medicine. PMID:34516913
Contraceptive and Infertility Target DataBase: a contraceptive drug development tool for targeting and analysis of human reproductive specific tissues†. PMID:34514504
Exploration of In-silico screening of therapeutic agents against SARS-CoV-2. PMID:34511699
Rapid prototyping of arbitrary 2D and 3D wireframe DNA origami. PMID:34508356
Pan-3C Protease Inhibitor Rupintrivir Binds SARS-CoV-2 Main Protease in a Unique Binding Mode. PMID:34506130
Structural Computational Analysis of the Natural History of Class I aminoacyl-tRNA Synthetases Suggests their Role in Establishing the Genetic Code. PMID:34505179
Effects of radiation damage and inelastic scattering on single-particle imaging of hydrated proteins with an X-ray Free-Electron Laser. PMID:34504156
Anthraquinolone and quinolizine derivatives as an alley of future treatment for COVID-19: an in silico machine learning hypothesis. PMID:34504128
Multilevel Approach for the Treatment of Giardiasis by Targeting Arginine Deiminase. PMID:34502400
Exploring the Binding Mechanism of PF-07321332 SARS-CoV-2 Protease Inhibitor through Molecular Dynamics and Binding Free Energy Simulations. PMID:34502033
A Structure Based Study of Selective Inhibition of Factor IXa over Factor Xa. PMID:34500804
Design, Synthesis and SAR in 2,4,7-Trisubstituted Pyrido[3,2-d]Pyrimidine Series as Novel PI3K/mTOR Inhibitors. PMID:34500781
Structural Insights and Docking Analysis of Adamantane-Linked 1,2,4-Triazole Derivatives as Potential 11β-HSD1 Inhibitors. PMID:34500764
Coumarins as Tool Compounds to Aid the Discovery of Selective Function Modulators of Steroid Hormone Binding Proteins. PMID:34500576
INTERCAAT: identifying interface residues between macromolecules. PMID:34499117
RPocket: an intuitive database of RNA pocket topology information with RNA-ligand data resources. PMID:34496744
Packpred: Predicting the Functional Effect of Missense Mutations. PMID:34490344
Identification of Hub Genes Related to Liver Metastasis of Colorectal Cancer by Integrative Analysis. PMID:34490113
Binding of regulatory proteins to nucleosomes is modulated by dynamic histone tails. PMID:34489435
3dRS, a Web-Based Tool to Share Interactive Representations of 3D Biomolecular Structures and Molecular Dynamics Trajectories. PMID:34485386
Structure-based identification of galectin-1 selective modulators in dietary food polyphenols: a pharmacoinformatics approach. PMID:34482478
Characterization of a novel multidomain CE15-GH8 enzyme encoded by a polysaccharide utilization locus in the human gut bacterium Bacteroides eggerthii. PMID:34480044
FORUM: Building a Knowledge Graph from public databases and scientific literature to extract associations between chemicals and diseases. PMID:34478489
Chalcogen Bonds Involving Selenium in Protein Structures. PMID:34477364
An Integrative Approach to Determine 3D Protein Structures Using Sparse Paramagnetic NMR Data and Physical Modeling. PMID:34476238
Differentiable molecular simulation can learn all the parameters in a coarse-grained force field for proteins. PMID:34473813
Vfold2D-MC: A Physics-Based Hybrid Model for Predicting RNA Secondary Structure Folding. PMID:34473508
Revealing the molecular interplay of curcumin as Culex pipiens Acetylcholine esterase 1 (AChE1) inhibitor. PMID:34471175
Drug repositioning for anti-tuberculosis drugs: an in silico polypharmacology approach. PMID:34468898
Ligand Strain Energy in Large Library Docking. PMID:34467754
LZerD Protein-Protein Docking Webserver Enhanced With de novo Structure Prediction. PMID:34466411
A quantitative model predicts how m6A reshapes the kinetic landscape of nucleic acid hybridization and conformational transitions. PMID:34465779
Exploring targets and signaling pathways of paeonol involved in relieving inflammation based on modern technology. PMID:34463943
On the roles of intrinsically disordered proteins and regions in cell communication and signaling. PMID:34461937
Identifying cysteine residues susceptible to oxidation by photoactivatable atomic oxygen precursors using a proteome-wide analysis. PMID:34458801
In silico molecular docking of SARS-CoV-2 surface proteins with microbial non-ribosomal peptides: identification of potential drugs. PMID:34456530
Synthesis and Cytotoxic Activity of Combretastatin A-4 and 2,3-Diphenyl-2H-indazole Hybrids. PMID:34451912
Reynoutria Rhizomes as a Natural Source of SARS-CoV-2 Mpro Inhibitors-Molecular Docking and In Vitro Study. PMID:34451839
Mechanism of noncoding RNA-associated N6-methyladenosine recognition by an RNA processing complex during IgH DNA recombination. PMID:34450044
Time-Lagged Independent Component Analysis of Random Walks and Protein Dynamics. PMID:34449229
Native structure of the RhopH complex, a key determinant of malaria parasite nutrient acquisition. PMID:34446549
Drug Discovery of Spinal Muscular Atrophy (SMA) from the Computational Perspective: A Comprehensive Review. PMID:34445667
PYTHIA: Deep Learning Approach for Local Protein Conformation Prediction. PMID:34445537
Betulin Sulfonamides as Carbonic Anhydrase Inhibitors and Anticancer Agents in Breast Cancer Cells. PMID:34445506
Computational Insight on the Interaction of Common Blood Proteins with Gold Nanoparticles. PMID:34445432
Tamoxifen Sensitizes Acute Lymphoblastic Leukemia Cells to Cannabidiol by Targeting Cyclophilin-D and Altering Mitochondrial Ca2+ Homeostasis. PMID:34445394
Graph Theoretical Methods and Workflows for Searching and Annotation of RNA Tertiary Base Motifs and Substructures. PMID:34445259
Non-Toxic Dimeric Peptides Derived from the Bothropstoxin-I Are Potent SARS-CoV-2 and Papain-like Protease Inhibitors. PMID:34443484
Synthesis, Biological Evaluation, and In Silico Studies of New Acetylcholinesterase Inhibitors Based on Quinoxaline Scaffold. PMID:34443482
Applications of Ionic Liquids in Whole-Cell and Isolated Enzyme Biocatalysis. PMID:34443378
Synthesis and Antiplasmodial Activity of Bisindolylcyclobutenediones. PMID:34443327
Identification of Novel Cathepsin B Inhibitors with Implications in Alzheimer's Disease: Computational Refining and Biochemical Evaluation. PMID:34440715
A Novel Missense Mutation in TNNI3K Causes Recessively Inherited Cardiac Conduction Disease in a Consanguineous Pakistani Family. PMID:34440456
Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review. PMID:34439912
Analysis of Carotenoids in Haloarchaea Species from Atacama Saline Lakes by High Resolution UHPLC-Q-Orbitrap-Mass Spectrometry: Antioxidant Potential and Biological Effect on Cell Viability. PMID:34439478
Computational Approaches for Cancer-Fighting: From Gene Expression to Functional Foods. PMID:34439361
A Y-linked anti-Müllerian hormone type-II receptor is the sex-determining gene in ayu, Plecoglossus altivelis. PMID:34437539
Shape-Restrained Modeling of Protein-Small-Molecule Complexes with High Ambiguity Driven DOCKing. PMID:34436890
UHPLC-MS Chemical Fingerprinting and Antioxidant, Antiproliferative, and Enzyme Inhibition Potential of Gaultheria pumila Berries. PMID:34436464
Neuroprotective Effect of Cyclo-(L-Pro-L-Phe) Isolated from the Jellyfish-Derived Fungus Aspergillus flavus. PMID:34436256
Exploring Covalent Docking Mechanisms of Boron-Based Inhibitors to Class A, C and D β-Lactamases Using Time-dependent Hybrid QM/MM Simulations. PMID:34434961
A Computational Approach to Evaluate the Combined Effect of SARS-CoV-2 RBD Mutations and ACE2 Receptor Genetic Variants on Infectivity: The COVID-19 Host-Pathogen Nexus. PMID:34434902
HPLC method to resolve, identify and quantify guanine nucleotides bound to recombinant ras GTPase. PMID:34433016
Data Mining and Systems Pharmacology to Elucidate Effectiveness and Mechanisms of Chinese Medicine in Treating Primary Liver Cancer. PMID:34432201
Discovery of novel MIF inhibitors that attenuate microglial inflammatory activation by structures-based virtual screening and in vitro bioassays. PMID:34429524
Mutation-induced changes in the receptor-binding interface of the SARS-CoV-2 Delta variant B.1.617.2 and implications for immune evasion. PMID:34425281
Fold2Seq: A Joint Sequence(1D)-Fold(3D) Embedding-based Generative Model for Protein Design. PMID:34423306
Structural and Genomic Insights Into Pyrazinamide Resistance in Mycobacterium tuberculosis Underlie Differences Between Ancient and Modern Lineages. PMID:34422898
Computational modeling reveals key molecular properties and dynamic behavior of disruptor of telomeric silencing 1-like (DOT1L) and partnering complexes involved in leukemogenesis. PMID:34414607
Comparative Analysis of Structural and Dynamical Features of Ribosome Upon Association With mRNA Reveals Potential Role of Ribosomal Proteins. PMID:34409066
Genomics-guided identification of potential modulators of SARS-CoV-2 entry proteases, TMPRSS2 and Cathepsins B/L. PMID:34407143
Immunopeptidomics toolkit library (IPTK): a python-based modular toolbox for analyzing immunopeptidomics data. PMID:34404349
Ganoderma applanatum mushroom provides new insights into the management of diabetes mellitus, hyperlipidemia, and hepatic degeneration: A comprehensive analysis. PMID:34401085
Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. PMID:34399188
PASSer: Prediction of Allosteric Sites Server. PMID:34396127
Network Pharmacology Approach for Predicting Targets of Zishen Yutai Pills on Premature Ovarian Insufficiency. PMID:34394393
Molecular modeling, docking and dynamics analysis of lipid droplet associated enzyme Ypr147cp from Saccharomyces cerevisiae. PMID:34393428
Computational studies reveal Fluorine based quinolines to be potent inhibitors for proteins involved in SARS-CoV-2 assembly. PMID:34393265
Sequence-specific dynamics of DNA response elements and their flanking sites regulate the recognition by AP-1 transcription factors. PMID:34387667
Synthesis and molecular docking study of novel COVID-19 inhibitors. PMID:34385863
Indole-3-Glycerol Phosphate Synthase From Mycobacterium tuberculosis: A Potential New Drug Target. PMID:34383995
Fold Evolution before LUCA: Common Ancestry of SH3 Domains and OB Domains. PMID:34383917
Protein inter-residue contact and distance prediction by coupling complementary coevolution features with deep residual networks in CASP14. PMID:34382712
Peptide bond planarity constrains hydrogen bond geometry and influences secondary structure conformations. PMID:34382009
GraphDTI: A robust deep learning predictor of drug-target interactions from multiple heterogeneous data. PMID:34380569
Spodium Bonds in Biological Systems: Expanding the Role of Zn in Protein Structure and Function. PMID:34375103
Pathogenic nsSNPs that increase the risks of cancers among the Orang Asli and Malays. PMID:34373545
Phosphoinositide Recognition Sites Are Blocked by Metabolite Attachment. PMID:34368138
Fluorescent Phthalocyanine-Encapsulated Bovine Serum Albumin Nanoparticles: Their Deployment as Therapeutic Agents in the NIR Region. PMID:34361832
Identification of Broad-Spectrum MMP Inhibitors by Virtual Screening. PMID:34361703
Design, Synthesis, and In Vitro Antiproliferative Activity of Hydantoin and Purine Derivatives with the 4-Acetylphenylpiperazinylalkyl Moiety. PMID:34361351
Using Budding Yeast to Identify Molecules That Block Cancer Cell 'Mitotic Slippage' Only in the Presence of Mitotic Poisons. PMID:34360748
Novel Purine Chemotypes with Activity against Plasmodium falciparum and Trypanosoma cruzi. PMID:34358064
Functional Effects In Silico Prediction for Androgen Receptor Ligand-Binding Domain Novel I836S Mutation. PMID:34357031
Identification of Potential Kinase Inhibitors within the PI3K/AKT Pathway of Leishmania Species. PMID:34356660
New Hybrid Compounds Combining Fragments of Usnic Acid and Monoterpenoids for Effective Tyrosyl-DNA Phosphodiesterase 1 Inhibition. PMID:34356597
Phosphorylation within Intrinsic Disordered Region Discriminates Histone Variant macroH2A1 Splicing Isoforms-macroH2A1.1 and macroH2A1.2. PMID:34356514
Chemical Composition, In Vitro and In Silico Antioxidant Potential of Melissa officinalis subsp. officinalis Essential Oil. PMID:34356313
Insights into the Binding of Intrinsically Disordered Proteins from Molecular Dynamics Simulation. PMID:34354764
Genome-wide analysis of HECT E3 ubiquitin ligase gene family in Solanum lycopersicum. PMID:34354159
Characterization of Five Transmembrane Proteins: With Focus on the Tweety, Sideroflexin, and YIP1 Domain Families. PMID:34350187
Vibrational spectroscopy, quantum computational and molecular docking studies on 2-chloroquinoline-3-carboxaldehyde. PMID:34345729
A375 melanoma cells are sensitized to cisplatin-induced toxicity by a synthetic nitro-flavone derivative 2-(4-Nitrophenyl)-4H-chromen-4-one through inhibition of PARP1. PMID:34342816
Carbonic anhydrase activation profile of indole-based derivatives. PMID:34340630
Emerging mutations in envelope protein of SARS-CoV-2 and their effect on thermodynamic properties. PMID:34337139
Binding affinity and mechanisms of SARS-CoV-2 variants. PMID:34336146
Haemoglobin switching modulator SNPs rs5006884 is associated with increased HbA2 in β-thalassaemia carriers. PMID:34336034
Discovery of a New CDK4/6 and PI3K/AKT Multiple Kinase Inhibitor Aminoquinol for the Treatment of Hepatocellular Carcinoma. PMID:34335258
Peculiar substrate specificity of δ1-pyrroline-5-carboxylate reductase in the obligately fermentative bacterium Zymomonas mobilis. PMID:34331182
Identification of non-classical hCA XII inhibitors using combination of computational approaches for drug design and discovery. PMID:34330958
Gram-negative outer-membrane proteins with multiple β-barrel domains. PMID:34330833
DNA end resection during homologous recombination. PMID:34329854
BRCA2 binding through a cryptic repeated motif to HSF2BP oligomers does not impact meiotic recombination. PMID:34326328
Analysis of folded structure and folding thermodynamics in heterogeneous-backbone proteomimetics. PMID:34325801
Taxallnomy: an extension of NCBI Taxonomy that produces a hierarchically complete taxonomic tree. PMID:34325658
Flavan-3-ol Microbial Metabolites Modulate Proteolysis in Neuronal Cells Reducing Amyloid-beta (1-42) Levels. PMID:34318994
Cyclic Stiffness Modulation of Cell-Laden Protein-Polymer Hydrogels in Response to User-Specified Stimuli including Light. PMID:34316509
Diverse Scientific Benchmarks for Implicit Membrane Energy Functions. PMID:34310137
In silico investigation to identify potential small molecule inhibitors of the RNA-dependent RNA polymerase (RdRp) nidovirus RdRp-associated nucleotidyltransferase domain. PMID:34305155
Prophylactic treatment with BX795 blocks activation of AKT and its downstream targets to protect vaginal keratinocytes and vaginal epithelium from HSV-2 infection. PMID:34303747
On the border of the amyloidogenic sequences: prefix analysis of the parallel beta sheets in the PDB_Amyloid collection. PMID:34303324
Memdock: An α-Helical Membrane Protein Docking Algorithm. PMID:34302673
Interface Prediction for GPCR Oligomerization Between Transmembrane Helices. PMID:34302672
Guardians of the Cell: State-of-the-Art of Membrane Proteins from a Computational Point-of-View. PMID:34302667
Support Vector Machine as a Supervised Learning for the Prioritization of Novel Potential SARS-CoV-2 Main Protease Inhibitors. PMID:34299333
Analysis of the Structural Mechanism of ATP Inhibition at the AAA1 Subunit of Cytoplasmic Dynein-1 Using a Chemical "Toolkit". PMID:34299323
A structure-based engineering approach to abrogate pre-existing antibody binding to biotherapeutics. PMID:34297759
Machine learning for enzyme engineering, selection and design. PMID:34296736
CHARMM-GUI LBS Finder & Refiner for Ligand Binding Site Prediction and Refinement. PMID:34296608
In silico DFT study, molecular docking, and ADMET predictions of cytidine analogs with antimicrobial and anticancer properties. PMID:34295612
SHH-N non-canonically sustains androgen receptor activity in androgen-independent prostate cancer cells. PMID:34290270
Genome-scale metabolic modeling reveals key features of a minimal gene set. PMID:34288418
DrugPred_RNA-A Tool for Structure-Based Druggability Predictions for RNA Binding Sites. PMID:34286972
Combining Well-Tempered Metadynamics Simulation and SPR Assays to Characterize the Binding Mechanism of the Universal T-Lymphocyte Tetanus Toxin Epitope TT830-843. PMID:34285916
Structure-based in silico approaches for drug discovery against Mycobacterium tuberculosis. PMID:34285773
Identification and Characterization of SRS Genes in Phaseolus vulgaris Genome and Their Responses Under Salt Stress. PMID:34282530
Drug discovery in the era of cryo-electron microscopy. PMID:34281791
Product Distributions of Cytochrome P450 OleTJE with Phenyl-Substituted Fatty Acids: A Computational Study. PMID:34281222
Structural Characterization of EnpA D,L-Endopeptidase from Enterococcus faecalis Prophage Provides Insights into Substrate Specificity of M23 Peptidases. PMID:34281200
Anti-platelet factor 4 antibodies causing VITT do not cross-react with SARS-CoV-2 spike protein. PMID:34280256
Atomic Resolution Homology Models and Molecular Dynamics Simulations of Plasmodium falciparum Tubulins. PMID:34278137
PPI-MASS: An Interactive Web Server to Identify Protein-Protein Interactions From Mass Spectrometry-Based Proteomics Data. PMID:34277709
Metabolite Profiling of Malaysian Gracilaria edulis Reveals Eplerenone as Novel Antibacterial Compound for Drug Repurposing Against MDR Bacteria. PMID:34276590
Motions around conserved helical weak spots facilitate GPCR activation. PMID:34272892
Metabolic Adaptations to Marine Environments: Molecular Diversity and Evolution of Ovothiol Biosynthesis in Bacteria. PMID:34272861
The Structure and Mechanism of Drug Transporters. PMID:34272696
Transcriptomic analysis and molecular docking reveal genes involved in the response of Aedes aegypti larvae to an essential oil extracted from Eucalyptus. PMID:34270558
OdoriFy: A conglomerate of artificial intelligence-driven prediction engines for olfactory decoding. PMID:34265305
Effects of nicotinic acetylcholine receptor-activating alkaloids on anxiety-like behavior in zebrafish. PMID:34264421
A conserved epitope III on hepatitis C virus E2 protein has alternate conformations facilitating cell binding or virus neutralization. PMID:34260404
Effect of dapagliflozin on diabetic patients with cardiovascular disease via MAPK signalling pathway. PMID:34258872
Safe-in-Man Broad Spectrum Antiviral Agents. PMID:34258746
Anticholinesterase Activity of Eight Medicinal Plant Species: In Vitro and In Silico Studies in the Search for Therapeutic Agents against Alzheimer's Disease. PMID:34257698
Diversity and function of arthropod endosymbiont toxins. PMID:34253453
Neuropilin-1 is required for endothelial cell adhesion to soluble vascular endothelial growth factor receptor 1. PMID:34252269
Caenorhabditis elegans RMI2 functional homolog-2 (RMIF-2) and RMI1 (RMH-1) have both overlapping and distinct meiotic functions within the BTR complex. PMID:34252074
An Azo Coupling-Based Chemoproteomic Approach to Systematically Profile the Tyrosine Reactivity in the Human Proteome. PMID:34251175
The Application of In Silico Methods on Umami Taste Receptor. PMID:34247277
Comparative Evaluation of Shape Retrieval Methods on Macromolecular Surfaces: An Application of Computer Vision Methods in Structural Bioinformatics. PMID:34247232
ClustENMD: Efficient sampling of biomolecular conformational space at atomic resolution. PMID:34240100
Study on the Molecular Mechanism of the Herbal Couple Sparganii Rhizoma-Curcumae Rhizoma in the Treatment of Lung Cancer Based on Network Pharmacology. PMID:34239587
In silico analysis of the aggregation propensity of the SARS-CoV-2 proteome: Insight into possible cellular pathologies. PMID:34237472
Cyclohexyl-α maltoside as a highly efficient tool for membrane protein studies. PMID:34235488
Shotgun EM of mycobacterial protein complexes during stationary phase stress. PMID:34235480
Crystal structure of MOA in complex with a peptide fragment: A protease caught in flagranti. PMID:34235469
Host-emitted amino acid cues regulate bacterial chemokinesis to enhance colonization. PMID:34233153
In-Cell Labeling and Mass Spectrometry for Systems-Level Structural Biology. PMID:34232610
Whole-exome imputation within UK Biobank powers rare coding variant association and fine-mapping analyses. PMID:34226706
An immunoinformatics approach to design a multi-epitope vaccine against Mycobacterium tuberculosis exploiting secreted exosome proteins. PMID:34226593
A computational multi-targeting approach for drug repositioning for psoriasis treatment. PMID:34225727
Impact of Structural Observables From Simulations to Predict the Effect of Single-Point Mutations in MHC Class II Peptide Binders. PMID:34222328
Novel antigen panel for modern broad-spectrum recombinant rotavirus A vaccine. PMID:34222124
3CLpro and PLpro affinity, a docking study to fight COVID19 based on 900 compounds from PubChem and literature. Are there new drugs to be found? PMID:34219808
Uncovering Membrane-Bound Models of Coagulation Factors by Combined Experimental and Computational Approaches. PMID:34214998
Chalcogen Bonds in Selenocysteine Seleninic Acid, a Functional GPx Constituent, and in Other Seleninic or Sulfinic Acid Derivatives. PMID:34214252
SidechainNet: An all-atom protein structure dataset for machine learning. PMID:34213059
Prospective Artificial Intelligence to Dissect the Dengue Immune Response and Discover Therapeutics. PMID:34211454
Bayesian optimization with evolutionary and structure-based regularization for directed protein evolution. PMID:34210336
Interactions of Chemically Synthesized Ferrihydrite Nanoparticles with Human Serum Transferrin: Insights from Fluorescence Spectroscopic Studies. PMID:34210014
Transamidation Down-Regulates Intestinal Immunity of Recombinant α-Gliadin in HLA-DQ8 Transgenic Mice. PMID:34209932
Synthesis and Antiviral Evaluation of Nucleoside Analogues Bearing One Pyrimidine Moiety and Two D-Ribofuranosyl Residues. PMID:34208647
Structural Insights into the Interactions of Digoxin and Na+/K+-ATPase and Other Targets for the Inhibition of Cancer Cell Proliferation. PMID:34208576
SRPassing Co-translational Targeting: The Role of the Signal Recognition Particle in Protein Targeting and mRNA Protection. PMID:34208095
How Does Bacillus thuringiensis Crystallize Such a Large Diversity of Toxins? PMID:34206796
Combined Naïve Bayesian, Chemical Fingerprints and Molecular Docking Classifiers to Model and Predict Androgen Receptor Binding Data for Environmentally- and Health-Sensitive Substances. PMID:34206613
17β-Estradiol-Induced Conformational Changes of Human Microsomal Triglyceride Transfer Protein: A Computational Molecular Modelling Study. PMID:34206252
Antiviral Activity of Two Marine Carotenoids against SARS-CoV-2 Virus Entry In Silico and In Vitro. PMID:34204256
Molecular Insight into the Regulation of Vimentin by Cysteine Modifications and Zinc Binding. PMID:34203497
Man-Specific Lectins from Plants, Fungi, Algae and Cyanobacteria, as Potential Blockers for SARS-CoV, MERS-CoV and SARS-CoV-2 (COVID-19) Coronaviruses: Biomedical Perspectives. PMID:34203435
Heparan Sulfate Binding Cationic Peptides Restrict SARS-CoV-2 Entry. PMID:34202835
'All That Glitters Is Not Gold': High-Resolution Crystal Structures of Ligand-Protein Complexes Need Not Always Represent Confident Binding Poses. PMID:34202053
Colombian Scorpion Centruroides margaritatus: Purification and Characterization of a Gamma Potassium Toxin with Full-Block Activity on the hERG1 Channel. PMID:34201318
Bioinformatics Accelerates the Major Tetrad: A Real Boost for the Pharmaceutical Industry. PMID:34201152
Toxic Metal Species and 'Endogenous' Metalloproteins at the Blood-Organ Interface: Analytical and Bioinorganic Aspects. PMID:34199902
Off-Target-Based Design of Selective HIV-1 PROTEASE Inhibitors. PMID:34199858
Elucidating the Mechanism of Action of the Attributed Immunomodulatory Role of Eltrombopag in Primary Immune Thrombocytopenia: An In Silico Approach. PMID:34199099
Structural characterization of two solute-binding proteins for N,N'-diacetylchitobiose/N,N',N''-triacetylchitotoriose of the gram-positive bacterium, Paenibacillus sp. str. FPU-7. PMID:34195603
Xiaoxuming Decoction Regulates Vascular Function by Modulating G Protein-Coupled Receptors: A Molecular Docking Study. PMID:34195269
In Silico Drug Screening Analysis against the Overexpression of PGAM1 Gene in Different Cancer Treatments. PMID:34195264
De novo Design of G Protein-Coupled Receptor 40 Peptide Agonists for Type 2 Diabetes Mellitus Based on Artificial Intelligence and Site-Directed Mutagenesis. PMID:34195182
Systematic Investigation of the Effect of Powerful Tianma Eucommia Capsule on Ischemic Stroke Using Network Pharmacology. PMID:34194527
A Repurposed Drug Screen Identifies Compounds That Inhibit the Binding of the COVID-19 Spike Protein to ACE2. PMID:34194331
Surprising Twists in Nucleosomal DNA with Implication for Higher-order Folding. PMID:34192585
Nanoscape, a data-driven 3D real-time interactive virtual cell environment. PMID:34191720
Functional inhibition of lactate dehydrogenase suppresses pancreatic adenocarcinoma progression. PMID:34185423
Thermodynamic Origin of Differential Excipient-Lysozyme Interactions. PMID:34179093
Information-Driven Docking for TCR-pMHC Complex Prediction. PMID:34177934
RosettaCM for antibodies with very long HCDR3s and low template availability. PMID:34176159
Compensatory epistasis explored by molecular dynamics simulations. PMID:34173867
Functional differences between TSHR alleles associate with variation in spawning season in Atlantic herring. PMID:34172814
A topology-based network tree for the prediction of protein-protein binding affinity changes following mutation. PMID:34170981
Predicting aptamer sequences that interact with target proteins using an aptamer-protein interaction classifier and a Monte Carlo tree search approach. PMID:34170922
Identification of known drugs as potential SARS-CoV-2 Mpro inhibitors using ligand- and structure-based virtual screening. PMID:34169729
A perspective on the molecular simulation of DNA from structural and functional aspects. PMID:34168783
Insights into the substrate binding mechanism of SULT1A1 through molecular dynamics with excited normal modes simulations. PMID:34162941
Validating TDP1 as an Inhibition Target for the Development of Chemosensitizers for Camptothecin-Based Chemotherapy Drugs. PMID:34159519
Tyr-Asp inhibition of glyceraldehyde 3-phosphate dehydrogenase affects plant redox metabolism. PMID:34156108
A variant in human AIOLOS impairs adaptive immunity by interfering with IKAROS. PMID:34155405
Elucidation of the molecular interactions that enable stable assembly and structural diversity in multicomponent immune receptors. PMID:34155106
The application of artificial intelligence and data integration in COVID-19 studies: a scoping review. PMID:34151987
Mapping the intellectual structure of the coronavirus field (2000-2020): a co-word analysis. PMID:34149117
The dual role of SrbA from Paracoccidioides lutzii: a hypoxic regulator. PMID:34148216
Entry-inhibitory role of catechins against SARS-CoV-2 and its UK variant. PMID:34147855
Peptides of H. sapiens and P. falciparum that are predicted to bind strongly to HLA-A*24:02 and homologous to a SARS-CoV-2 peptide. PMID:34146538
Learning the protein language: Evolution, structure, and function. PMID:34139171
The N-terminal Helix-Turn-Helix Motif of Transcription Factors MarA and Rob Drives DNA Recognition. PMID:34137249
ADAMTS1, MPDZ, MVD, and SEZ6: candidate genes for autosomal recessive nonsyndromic hearing impairment. PMID:34135477
Development and Evaluation of GlycanDock: A Protein-Glycoligand Docking Refinement Algorithm in Rosetta. PMID:34133179
Binding of single-mutant epidermal growth factor (EGF) ligands alters the stability of the EGF receptor dimer and promotes growth signaling. PMID:34126069
Improving Docking Power for Short Peptides Using Random Forest. PMID:34124893
Unveiling the molecular mechanism of SARS-CoV-2 main protease inhibition from 137 crystal structures using algebraic topology and deep learning. PMID:34123218
Graph neural network based coarse-grained mapping prediction. PMID:34123175
Accurate prediction of chemical shifts for aqueous protein structure on "Real World" data. PMID:34122823
Heterologous expression of cyanobacterial PCS confers augmented arsenic and cadmium stress tolerance and higher artemisinin in Artemisia annua hairy roots. PMID:34122662
Toward the solution of the protein structure prediction problem. PMID:34119522
Quantitative description of a contractile macromolecular machine. PMID:34117062
Identifying biophysical assays and in silico properties that enrich for slow clearance in clinical-stage therapeutic antibodies. PMID:34116620
Interaction of selected terpenoids with two SARS-CoV-2 key therapeutic targets: An in silico study through molecular docking and dynamics simulations. PMID:34116362
LigTMap: ligand and structure-based target identification and activity prediction for small molecular compounds. PMID:34112240
Structural and Dynamical Differences in the Spike Protein RBD in the SARS-CoV-2 Variants B.1.1.7 and B.1.351. PMID:34110159
Scrutinizing Coronaviruses Using Publicly Available Bioinformatic Tools: The Viral Structural Proteins as a Case Study. PMID:34109214
Ecology of inorganic sulfur auxiliary metabolism in widespread bacteriophages. PMID:34108477
GNINA 1.0: molecular docking with deep learning. PMID:34108002
Virtual screening on the web for drug repurposing: a primer. PMID:34104664
Screening of world approved drugs against highly dynamical spike glycoprotein of SARS-CoV-2 using CaverDock and machine learning. PMID:34104357
Identification of anti-Parkinson's Disease Lead Compounds from Aspergillus ochraceus Targeting Adenosin Receptors A2A. PMID:34102706
Assessment of protein-protein interfaces in cryo-EM derived assemblies. PMID:34099703
Dynamic Molecular Evolution of Mammalian Homeobox Genes: Duplication, Loss, Divergence and Gene Conversion Sculpt PRD Class Repertoires. PMID:34097121
Redefining Protein Interfaces within Protein Single Crystals with DNA. PMID:34096291
Design of New Schiff-Base Copper(II) Complexes: Synthesis, Crystal Structures, DFT Study, and Binding Potency toward Cytochrome P450 3A4. PMID:34095663
Speculative assessment, molecular composition, PDOS, topology exploration (ELF, LOL, RDG), ligand-protein interactions, on 5-bromo-3-nitropyridine-2-carbonitrile. PMID:34095571
Computational Modeling as a Tool to Investigate PPI: From Drug Design to Tissue Engineering. PMID:34095231
Chemical synthesis of human syndecan-4 glycopeptide bearing O-, N-sulfation and multiple aspartic acids for probing impacts of the glycan chain and the core peptide on biological functions. PMID:34094105
Pharmacological inhibition of noncanonical EED-EZH2 signaling overcomes chemoresistance in prostate cancer. PMID:34093859
Aquaporins in insulin resistance and diabetes: More than channels! PMID:34090243
SARS-Cov2 S Protein Features Potential Estrogen Binding Site. PMID:34084077
Metadynamics-Based Approaches for Modeling the Hypoxia-Inducible Factor 2α Ligand Binding Process. PMID:34082524
Exploring aromatic cage flexibility of the histone methyllysine reader protein Spindlin1 and its impact on binding mode prediction: an in silico study. PMID:34081238
SIRT6 transcriptionally regulates fatty acid transport by suppressing PPARγ. PMID:34077730
Regulation of Glycine Cleavage and Detoxification by a Highly Conserved Glycine Riboswitch in Burkholderia spp. PMID:34076709
Mechnetor: a web server for exploring protein mechanism and the functional context of genetic variants. PMID:34076240
Combination of consensus and ensemble docking strategies for the discovery of human dihydroorotate dehydrogenase inhibitors. PMID:34075175
NAD(H)-mediated tetramerization controls the activity of Legionella pneumophila phospholipase PlaB. PMID:34074754
4-Arylthiosemicarbazide derivatives as a new class of tyrosinase inhibitors and anti-Toxoplasma gondii agents. PMID:34074198
Deep Learning-Based Advances in Protein Structure Prediction. PMID:34074028
Characterization of an Endolysin Targeting Clostridioides difficile That Affects Spore Outgrowth. PMID:34073633
Structure-Based Design, Docking and Binding Free Energy Calculations of A366 Derivatives as Spindlin1 Inhibitors. PMID:34072837
Development of Halogenated Pyrazolines as Selective Monoamine Oxidase-B Inhibitors: Deciphering via Molecular Dynamics Approach. PMID:34071665
Computational Study on Temperature Driven Structure-Function Relationship of Polysaccharide Producing Bacterial Glycosyl Transferase Enzyme. PMID:34071348
Prediction and Evolution of the Molecular Fitness of SARS-CoV-2 Variants: Introducing SpikePro. PMID:34070055
Global Genomic Analysis of SARS-CoV-2 RNA Dependent RNA Polymerase Evolution and Antiviral Drug Resistance. PMID:34069681
Force Field Parameters for Fe2+4S2-4 Clusters of Dihydropyrimidine Dehydrogenase, the 5-Fluorouracil Cancer Drug Deactivation Protein: A Step towards In Silico Pharmacogenomics Studies. PMID:34069161
Regulation of the Phosphoinositide Code by Phosphorylation of Membrane Readers. PMID:34069055
Bacterial Resistance to Antimicrobial Agents. PMID:34067579
KEAP1 Cancer Mutants: A Large-Scale Molecular Dynamics Study of Protein Stability. PMID:34065616
Pepscan Approach for the Identification of Protein-Protein Interfaces: Lessons from Experiment. PMID:34063976
A Bittersweet Computational Journey among Glycosaminoglycans. PMID:34063530
Structure-Based and Rational Design of a Hepatitis C Virus Vaccine. PMID:34063143
Sphingomonas sp. KT-1 PahZ2 Structure Reveals a Role for Conformational Dynamics in Peptide Bond Hydrolysis. PMID:34060838
Advances and perspectives in discovery and functional analysis of small secreted proteins in plants. PMID:34059650
Conformational epitope matching and prediction based on protein surface spiral features. PMID:34058977
Plausible blockers of Spike RBD in SARS-CoV2-molecular design and underlying interaction dynamics from high-level structural descriptors. PMID:34057647
Addressing the Exigent Role of a Coumarin Fluorophore toward Finding the Suitable Microenvironment of Biomimicking and Biomolecular Systems: Steering to Project the Drug Designing and Drug Delivery Study. PMID:34056342
Substrate Selectivity of Coumarin Derivatives by Human CYP1 Enzymes: In Vitro Enzyme Kinetics and In Silico Modeling. PMID:34056284
Dasatinib-SIK2 Binding Elucidated by Homology Modeling, Molecular Docking, and Dynamics Simulations. PMID:34056256
Computational Screening of Potential Inhibitors of Desulfobacter postgatei for Pyrite Scale Prevention in Oil and Gas Wells. PMID:34056214
Mechanisms and Neuroprotective Activities of Stigmasterol Against Oxidative Stress-Induced Neuronal Cell Death via Sirtuin Family. PMID:34055852
Systems Pharmacology and In Silico Docking Analysis Uncover Association of CA2, PPARG, RXRA, and VDR with the Mechanisms Underlying the Shi Zhen Tea Formula Effect on Eczema. PMID:34055023
MTR3D: identifying regions within protein tertiary structures under purifying selection. PMID:34050760
Pretraining model for biological sequence data. PMID:34050350
IUPred3: prediction of protein disorder enhanced with unambiguous experimental annotation and visualization of evolutionary conservation. PMID:34048569
A large-scale comparative study on peptide encodings for biomedical classification. PMID:34046590
Recent Advances in Protein Homology Detection Propelled by Inter-Residue Interaction Map Threading. PMID:34046429
Development of a cobalt(iii)-based ponatinib prodrug system. PMID:34046181
Prospective Role of Peptide-Based Antiviral Therapy Against the Main Protease of SARS-CoV-2. PMID:34041263
An Integrated Analysis of Network Pharmacology, Molecular Docking, and Experiment Validation to Explore the New Candidate Active Component and Mechanism of Cuscutae Semen-Mori Fructus Coupled-Herbs in Treating Oligoasthenozoospermia. PMID:34040346
Structure-based protein function prediction using graph convolutional networks. PMID:34039967
Protein model accuracy estimation empowered by deep learning and inter-residue distance prediction in CASP14. PMID:34035363
Modelling of an autonomous Nav1.5 channel system as a part of in silico pharmacology study. PMID:34031769
On the effect of phylogenetic correlations in coevolution-based contact prediction in proteins. PMID:34029316
Structural Analysis of Strigolactone-Related Gene Products. PMID:34028692
Mimosine functionalized gold nanoparticles (Mimo-AuNPs) suppress β-amyloid aggregation and neuronal toxicity. PMID:34027236
Structure-Guided Computational Approaches to Unravel Druggable Proteomic Landscape of Mycobacterium leprae. PMID:34026836
DESP: Deep Enhanced Sampling of Proteins' Conformation Spaces Using AI-Inspired Biasing Forces. PMID:34026817
Phytochemical Moieties From Indian Traditional Medicine for Targeting Dual Hotspots on SARS-CoV-2 Spike Protein: An Integrative in-silico Approach. PMID:34026798
Computational modeling and bioinformatic analyses of functional mutations in drug target genes in Mycobacterium tuberculosis. PMID:34025934
Non-competitive interactions between hydroxychloroquine and azithromycin: Systematic density functional, molecular dynamics, and docking calculations. PMID:34024911
LigAdvisor: a versatile and user-friendly web-platform for drug design. PMID:34023895
The interaction of the bioflavonoids with five SARS-CoV-2 proteins targets: An in silico study. PMID:34020130
Sequence analysis of tyrosine recombinases allows annotation of mobile genetic elements in prokaryotic genomes. PMID:34018328
COVID-19 biomarkers and their overlap with comorbidities in a disease biomarker data model. PMID:34015823
Utilizing graph machine learning within drug discovery and development. PMID:34013350
In silico binding profile characterization of SARS-CoV-2 spike protein and its mutants bound to human ACE2 receptor. PMID:34013346
Identification of Potential Binders of Mtb Universal Stress Protein (Rv1636) Through an in silico Approach and Insights Into Compound Selection for Experimental Validation. PMID:34012976
RGS5-TGFβ-Smad2/3 axis switches pro- to anti-apoptotic signaling in tumor-residing pericytes, assisting tumor growth. PMID:34012071
Unraveling the unbinding pathways of SARS-CoV-2 Papain-like proteinase known inhibitors by Supervised Molecular Dynamics simulation. PMID:34010326
Chimeric Phi29 DNA polymerase with helix-hairpin-helix motifs shows enhanced salt tolerance and replication performance. PMID:34009743
The Role of Cyclodextrins against Interface-Induced Denaturation in Pharmaceutical Formulations: A Molecular Dynamics Approach. PMID:33999634
Molecular Evolution of DNA Topoisomerase III Beta (TOP3B) in Metazoa. PMID:33999213
PredictProtein - Predicting Protein Structure and Function for 29 Years. PMID:33999203
Computational generation of proteins with predetermined three-dimensional shapes using ProteinSolver. PMID:33997819
Network Pharmacology-Based Investigation of the Therapeutic Mechanisms of Action of Danning Tablets in Nonalcoholic Fatty Liver Disease. PMID:33995543
Inhibition of SARS-CoV-2 reproduction using Boswellia carterii: A theoretical study. PMID:33994607
Systematic in silico Evaluation of Leishmania spp. Proteomes for Drug Discovery. PMID:33987166
A novel dual HDAC and HSP90 inhibitor, MPT0G449, downregulates oncogenic pathways in human acute leukemia in vitro and in vivo. PMID:33986242
Comparison of structure- and ligand-based scoring functions for deep generative models: a GPCR case study. PMID:33985583
Open-access data: A cornerstone for artificial intelligence approaches to protein structure prediction. PMID:33984281
Can molecular dynamics simulations improve the structural accuracy and virtual screening performance of GPCR models? PMID:33983933
Molecular dynamics shows complex interplay and long-range effects of post-translational modifications in yeast protein interactions. PMID:33979327
ProteinLens: a web-based application for the analysis of allosteric signalling on atomistic graphs of biomolecules. PMID:33978752
Modernized uniform representation of carbohydrate molecules in the Protein Data Bank. PMID:33978738
PhosIDP: a web tool to visualize the location of phosphorylation sites in disordered regions. PMID:33976270
The temperature-dependent conformational ensemble of SARS-CoV-2 main protease (Mpro). PMID:33972941
ModFlex: Towards Function Focused Protein Modeling. PMID:33972023
Improving the specificity of organophosphorus hydrolase to acephate by mutagenesis at its binding site: a computational study. PMID:33970322
Biallelic variants in HPDL cause pure and complicated hereditary spastic paraplegia. PMID:33970200
A putative novel starch-binding domain revealed by in silico analysis of the N-terminal domain in bacterial amylomaltases from the family GH77. PMID:33968573
Analysis of natural compounds against the activity of SARS-CoV-2 NSP15 protein towards an effective treatment against COVID-19: a theoretical and computational biology approach. PMID:33963942
Dual proteome-scale networks reveal cell-specific remodeling of the human interactome. PMID:33961781
Improving deep learning-based protein distance prediction in CASP14. PMID:33961009
Structural genomics and the Protein Data Bank. PMID:33957120
Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures. PMID:33956157
Clinical Manifestations, Mutational Analysis, and Immunological Phenotype in Patients with RAG1/2 Mutations: First Cases Series from Mexico and Description of Two Novel Mutations. PMID:33954879
EMNUSS: a deep learning framework for secondary structure annotation in cryo-EM maps. PMID:33954706
Structure elements can be predicted using the contact volume among protein residues. PMID:33954082
Structural insights into protein folding, stability and activity using in vivo perdeuteration of hen egg-white lysozyme. PMID:33953924
Interactions and effects of food additive dye Allura red on pepsin structure and protease activity; experimental and computational supports. PMID:33953775
Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. PMID:33951211
On the use of multiple-time-step algorithms to save computing effort in molecular dynamics simulations of proteins. PMID:33951201
Bridging between material properties of proteins and the underlying molecular interactions. PMID:33951045
Computational Methods for the Elucidation of Protein Structure and Interactions. PMID:33950383
The Protein Data Bank Archive. PMID:33950382
PLIP 2021: expanding the scope of the protein-ligand interaction profiler to DNA and RNA. PMID:33950214
Metabolic bifunctionality of Rv0812 couples folate and peptidoglycan biosynthesis in Mycobacterium tuberculosis. PMID:33950161
Costunolide suppresses melanoma growth via the AKT/mTOR pathway in vitro and in vivo. PMID:33948365
Engineering the Modular Receptor-Binding Proteins of Klebsiella Phages Switches Their Capsule Serotype Specificity. PMID:33947754
Bioinformatic Prediction of Signaling Pathways for Apurinic/Apyrimidinic Endodeoxyribonuclease 1 (APEX1) and Its Role in Cholangiocarcinoma Cells. PMID:33946672
Computational Identification of Potential Anti-Inflammatory Natural Compounds Targeting the p38 Mitogen-Activated Protein Kinase (MAPK): Implications for COVID-19-Induced Cytokine Storm. PMID:33946644
A PSGL-1 glycomimetic reduces thrombus burden without affecting hemostasis. PMID:33945603
Analysis of electrostatic coupling throughout the laboratory evolution of a designed retroaldolase. PMID:33938058
Protein folding - seeing is deceiving. PMID:33938055
Identifying the challenges in implementing open science [version 1; peer review: 2 approved]. PMID:33937623
Detecting Protein Communities in Native Cell Extracts by Machine Learning: A Structural Biologist's Perspective. PMID:33937337
Carbonic Anhydrase in Pacific Abalone Haliotis discus hannai: Characterization, Expression, and Role in Biomineralization. PMID:33937335
Therapeutic development by repurposing drugs targeting SARS-CoV-2 spike protein interactions by simulation studies. PMID:33935562
Integrated Biophysical Modeling of the SARS-CoV-2 Spike Protein Binding and Allosteric Interactions with Antibodies. PMID:33929853
Rare germline variants in the E-cadherin gene CDH1 are associated with the risk of brain tumors of neuroepithelial and epithelial origin. PMID:33929593
How anisotropic and isotropic atomic displacement parameters monitor protein covalent bonds rigidity: isotropic B-factors underestimate bond rigidity. PMID:33928454
Alantolactone inhibits cervical cancer progression by downregulating BMI1. PMID:33927214
Searching for universal model of amyloid signaling motifs using probabilistic context-free grammars. PMID:33926372
AC2: An Efficient Protein Sequence Compression Tool Using Artificial Neural Networks and Cache-Hash Models. PMID:33925812
Multiscale Virtual Screening Optimization for Shotgun Drug Repurposing Using the CANDO Platform. PMID:33925237
Divergence Entropy-Based Evaluation of Hydrophobic Core in Aggressive and Resistant Forms of Transthyretin. PMID:33924717
Prolactin-Releasing Peptide Differentially Regulates Gene Transcriptomic Profiles in Mouse Bone Marrow-Derived Macrophages. PMID:33923285
Deep Learning in Virtual Screening: Recent Applications and Developments. PMID:33922714
Functional Interfaces, Biological Pathways, and Regulations of Interferon-Related DNA Damage Resistance Signature (IRDS) Genes. PMID:33922087
Coumarin-Chalcone Hybrids as Inhibitors of MAO-B: Biological Activity and In Silico Studies. PMID:33921982
Quinazoline Derivatives Designed as Efflux Pump Inhibitors: Molecular Modeling and Spectroscopic Studies. PMID:33921798
Phosphorylation, Mg-ADP, and Inhibitors Differentially Shape the Conformational Dynamics of the A-Loop of Aurora-A. PMID:33921540
Computational Design and Development of Benzodioxane-Benzamides as Potent Inhibitors of FtsZ by Exploring the Hydrophobic Subpocket. PMID:33920895
In Silico and In Vitro Evaluation of the Antimicrobial and Antioxidant Potential of Mentha × smithiana R. GRAHAM Essential Oil from Western Romania. PMID:33918674
Thiosemicarbazide Derivatives Decrease the ATPase Activity of Staphylococcus aureus Topoisomerase IV, Inhibit Mycobacterial Growth, and Affect Replication in Mycobacterium smegmatis. PMID:33918623
Native Structure-Based Peptides as Potential Protein-Protein Interaction Inhibitors of SARS-CoV-2 Spike Protein and Human ACE2 Receptor. PMID:33918595
Isolation, Structure Elucidation and In Silico Prediction of Potential Drug-Like Flavonoids from Onosma chitralicum Targeted towards Functionally Important Proteins of Drug-Resistant Bad Bugs. PMID:33918531
Experimental and Computational Studies on Structure and Energetic Properties of Halogen Derivatives of 2-Deoxy-D-Glucose. PMID:33918425
Synthesis, Characterization of Chitosan-Aluminum Oxide Nanocomposite for Green Synthesis of Annulated Imidazopyrazol Thione Derivatives. PMID:33916381
Molecular Dynamics-From Small Molecules to Macromolecules. PMID:33916359
Promising phytochemicals of traditional Himalayan medicinal plants against putative replication and transmission targets of SARS-CoV-2 by computational investigation. PMID:33915361
Detection of Binding Sites on SARS-CoV-2 Spike Protein Receptor-Binding Domain by Molecular Dynamics Simulations in Mixed Solvents. PMID:33914685
Synergistic DNA- and Protein-Based Recognition Promote an RNA-Templated Bio-orthogonal Reaction. PMID:33914384
A survey of the kinome pharmacopeia reveals multiple scaffolds and targets for the development of novel anthelmintics. PMID:33911106
Comparison of cellooligosaccharide conformations in complexes with proteins with energy maps for cellobiose. PMID:33910736
Risk of rapid evolutionary escape from biomedical interventions targeting SARS-CoV-2 spike protein. PMID:33909660
In silico structure-based discovery of a SARS-CoV-2 main protease inhibitor. PMID:33907519
Recognizing and validating ligands with CheckMyBlob. PMID:33905501
Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator. PMID:33904398
Protlego: A Python package for the analysis and design of chimeric proteins. PMID:33901273
Comparative Perturbation-Based Modeling of the SARS-CoV-2 Spike Protein Binding with Host Receptor and Neutralizing Antibodies: Structurally Adaptable Allosteric Communication Hotspots Define Spike Sites Targeted by Global Circulating Mutations. PMID:33900725
BIO-GATS: A Tool for Automated GPCR Template Selection Through a Biophysical Approach for Homology Modeling. PMID:33898512
The language of proteins: NLP, machine learning & protein sequences. PMID:33897979
Thiocyanate and Organic Carbon Inputs Drive Convergent Selection for Specific Autotrophic Afipia and Thiobacillus Strains Within Complex Microbiomes. PMID:33897653
Combined use of the hepatitis C drugs and amentoflavone could interfere with binding of the spike glycoprotein of SARS-CoV-2 to ACE2: the results of a molecular simulation study. PMID:33896392
Computational design and modeling of nanobodies toward SARS-CoV-2 receptor binding domain. PMID:33894099
mmCSM-PPI: predicting the effects of multiple point mutations on protein-protein interactions. PMID:33893812
Reverse vaccinology and subtractive genomics approaches for identifying common therapeutics against Mycobacterium leprae and Mycobacterium lepromatosis. PMID:33889182
Prediction of Anti-COVID 19 Therapeutic Power of Medicinal Moroccan Plants Using Molecular Docking. PMID:33888980
Cyclooxygenase-2 Inhibitor Parecoxib Was Disclosed as a PPAR-γ Agonist by In Silico and In Vitro Assay. PMID:33883322
Wolfram-like syndrome with bicuspid aortic valve due to a homozygous missense variant in CDK13. PMID:33879837
Preparing Membrane Proteins for Simulation Using CHARMM-GUI. PMID:33877631
Comparative transcriptomics and network pharmacology analysis to identify the potential mechanism of celastrol against osteoarthritis. PMID:33870466
Exploring the antidiabetic potential of compounds isolated from Anacardium occidentale using computational aproach: ligand-based virtual screening. PMID:33868895
In Silico Identification of Multi-target Anti-SARS-CoV-2 Peptides from Quinoa Seed Proteins. PMID:33867899
Scoring Functions for Protein-RNA Complex Structure Prediction: Advances, Applications, and Future Directions. PMID:33867869
Eudiplozoon nipponicum (Monogenea, Diplozoidae) and its adaptation to haematophagy as revealed by transcriptome and secretome profiling. PMID:33858339
Development of flexible electrochemical impedance spectroscopy-based biosensing platform for rapid screening of SARS-CoV-2 inhibitors. PMID:33857754
Universal Constraints on Protein Evolution in the Long-Term Evolution Experiment with Escherichia coli. PMID:33856016
Comprehensive omic characterization of breast cancer in Mexican-Hispanic women. PMID:33854067
Discovery of novel potential KIT inhibitors for the treatment of gastrointestinal stromal tumor. PMID:33851030
Characterization of amino acid residues of T-cell receptors interacting with HLA-A*02-restricted antigen peptides. PMID:33850892
A systematic approach to inserting split inteins for Boolean logic gate engineering and basal activity reduction. PMID:33850130
Essential oils as an effective alternative for the treatment of COVID-19: Molecular interaction analysis of protease (Mpro) with pharmacokinetics and toxicological properties. PMID:33848890
Inhibition of SARS-CoV-2 main protease: a repurposing study that targets the dimer interface of the protein. PMID:33847241
USP24 promotes drug resistance during cancer therapy. PMID:33846536
Targeting Acute Myelogenous Leukemia Using Potent Human Dihydroorotate Dehydrogenase Inhibitors Based on the 2-Hydroxypyrazolo[1,5-a]pyridine Scaffold: SAR of the Biphenyl Moiety. PMID:33844533
Structure-based identification of SARS-CoV-2 main protease inhibitors from anti-viral specific chemical libraries: an exhaustive computational screening approach. PMID:33844135
Computational molecular docking and virtual screening revealed promising SARS-CoV-2 drugs. PMID:33842834
Epigallocathechin-O-3-Gallate Inhibits Trypanothione Reductase of Leishmania infantum, Causing Alterations in Redox Balance and Leading to Parasite Death. PMID:33842389
A review on compound-protein interaction prediction methods: Data, format, representation and model. PMID:33841755
Rational design of flavonoid based potential inhibitors targeting SARS-CoV 3CL protease for the treatment of COVID-19. PMID:33840835
Computational evaluation of interactions between olfactory receptor OR2W1 and its ligands. PMID:33840173
Developments in solution-state NMR yield broader and deeper views of the dynamic ensembles of nucleic acids. PMID:33836446
Developing a macromolecular crystallography driven CURE. PMID:33834085
Neuropsychiatric Symptoms of COVID-19 Explained by SARS-CoV-2 Proteins' Mimicry of Human Protein Interactions. PMID:33833673
Identifying metal binding amino acids based on backbone geometries as a tool for metalloprotein engineering. PMID:33829594
Understanding the influence of lipid bilayers and ligand molecules in determining the conformational dynamics of somatostatin receptor 2. PMID:33828200
Learning the molecular grammar of protein condensates from sequence determinants and embeddings. PMID:33827920
Prefusion F-Based Polyanhydride Nanovaccine Induces Both Humoral and Cell-Mediated Immunity Resulting in Long-Lasting Protection against Respiratory Syncytial Virus. PMID:33827894
Quantifying evolutionary importance of protein sites: A Tale of two measures. PMID:33826605
Identification of doxorubicin as a potential therapeutic against SARS-CoV-2 (COVID-19) protease: a molecular docking and dynamics simulation studies. PMID:33826483
Protein identification from electron cryomicroscopy maps by automated model building and side-chain matching. PMID:33825706
Clinical Acquired Resistance to KRASG12C Inhibition through a Novel KRAS Switch-II Pocket Mutation and Polyclonal Alterations Converging on RAS-MAPK Reactivation. PMID:33824136
Adhatoda Vasica attenuates inflammatory and hypoxic responses in preclinical mouse models: potential for repurposing in COVID-19-like conditions. PMID:33823870
JMJD6 Is a Druggable Oxygenase That Regulates AR-V7 Expression in Prostate Cancer. PMID:33822745
Repurposing of approved drugs with potential to interact with SARS-CoV-2 receptor. PMID:33817352
Enhancement of conformational B-cell epitope prediction using CluSMOTE. PMID:33816926
A SARS-CoV-2 -human metalloproteome interaction map. PMID:33813307
Aromatic Rings as Molecular Determinants for the Molecular Recognition of Protein Kinase Inhibitors. PMID:33810025
Linear B-Cell Epitope Prediction for In Silico Vaccine Design: A Performance Review of Methods Available via Command-Line Interface. PMID:33809918
PepFun: Open Source Protocols for Peptide-Related Computational Analysis. PMID:33809815
The mwtab Python Library for RESTful Access and Enhanced Quality Control, Deposition, and Curation of the Metabolomics Workbench Data Repository. PMID:33808985
Two Key Amino Acids Variant of α-l-arabinofuranosidase from Bacillus subtilis Str. 168 with Altered Activity for Selective Conversion Ginsenoside Rc to Rd. PMID:33808840
Discovery of Novel Sultone Fused Berberine Derivatives as Promising Tdp1 Inhibitors. PMID:33808389
Structural Basis for the Functional Changes by EGFR Exon 20 Insertion Mutations. PMID:33807850
SARS-CoV-2 Main Protease Active Site Ligands in the Human Metabolome. PMID:33807773
Luteolin-Fabricated ZnO Nanostructures Showed PLK-1 Mediated Anti-Breast Cancer Activity. PMID:33807771
Mutations of Intrinsically Disordered Protein Regions Can Drive Cancer but Lack Therapeutic Strategies. PMID:33806614
A Holistic Evolutionary and 3D Pharmacophore Modelling Study Provides Insights into the Metabolism, Function, and Substrate Selectivity of the Human Monocarboxylate Transporter 4 (hMCT4). PMID:33805725
The Biological Significance of Targeting Acetylation-Mediated Gene Regulation for Designing New Mechanistic Tools and Potential Therapeutics. PMID:33803759
Patterns in Protein Flexibility: A Comparison of NMR "Ensembles", MD Trajectories, and Crystallographic B-Factors. PMID:33803249
Inhibitor Development against p7 Channel in Hepatitis C Virus. PMID:33802584
Bioinformatic Analysis of the Nicotinamide Binding Site in Poly(ADP-Ribose) Polymerase Family Proteins. PMID:33801950
Development of Novel Inhibitors Targeting the D-Box of the DNA Binding Domain of Androgen Receptor. PMID:33801338
Sofosbuvir Selects for Drug-Resistant Amino Acid Variants in the Zika Virus RNA-Dependent RNA-Polymerase Complex In Vitro. PMID:33800884
Diphenyl-Methane Based Thyromimetic Inhibitors for Transthyretin Amyloidosis. PMID:33800546
In Silico Investigation of Potential Applications of Gamma Carbonic Anhydrases as Catalysts of CO2 Biomineralization Processes: A Visit to the Thermophilic Bacteria Persephonella hydrogeniphila, Persephonella marina, Thermosulfidibacter takaii, and Thermus thermophilus. PMID:33799806
Cross-Talk between Overlap Interactions in Biomolecules: A Case Study of the β-Turn Motif. PMID:33799657
Inspecting the Mechanism of Fragment Hits Binding on SARS-CoV-2 Mpro by Using Supervised Molecular Dynamics (SuMD) Simulations. PMID:33797868
Novel mutations in NSP-1 and PLPro of SARS-CoV-2 NIB-1 genome mount for effective therapeutics. PMID:33797663
Neuroprotective and Neurorescue Mode of Action of Bacopa monnieri (L.) Wettst in 1-Methyl-4-phenyl-1,2,3,6-tetrahydropyridine-Induced Parkinson's Disease: An In Silico and In Vivo Study. PMID:33796021
Study of Combinatorial Drug Synergy of Novel Acridone Derivatives With Temozolomide Using in-silico and in-vitro Methods in the Treatment of Drug-Resistant Glioma. PMID:33791212
Biological Functions of RBP4 and Its Relevance for Human Diseases. PMID:33790810
c-di-AMP, a likely master regulator of bacterial K+ homeostasis machinery, activates a K+ exporter. PMID:33790011
Using the antibody-antigen binding interface to train image-based deep neural networks for antibody-epitope classification. PMID:33780441
Reconstruction of ARNT PAS-B Unfolding Pathways by Steered Molecular Dynamics and Artificial Neural Networks. PMID:33780250
In silico analysis of phylogeny, structure, and function of arsenite oxidase from unculturable microbiome of arsenic contaminated soil. PMID:33779860
Functional alterations by a subgroup of neonicotinoid pesticides in human dopaminergic neurons. PMID:33778899
Computational Analysis of Residue-Specific Binding Free Energies of Androgen Receptor to Ligands. PMID:33778009
Influence of Disease-Causing Mutations on Protein Structural Networks. PMID:33778000
QSAR Modeling for Multi-Target Drug Discovery: Designing Simultaneous Inhibitors of Proteins in Diverse Pathogenic Parasites. PMID:33777898
Structure-based molecular modeling in SAR analysis and lead optimization. PMID:33777339
Disease variants of human Δ1-pyrroline-5-carboxylate reductase 2 (PYCR2). PMID:33771508
NaV1.2 EFL domain allosterically enhances Ca2+ binding to sites I and II of WT and pathogenic calmodulin mutants bound to the channel CTD. PMID:33770503
Basigin drives intracellular accumulation of l-lactate by harvesting protons and substrate anions. PMID:33770122
Discovery of New Protein Targets of BPA Analogs and Derivatives Associated with Noncommunicable Diseases: A Virtual High-Throughput Screening. PMID:33769846
Prediction and Validation of a Druggable Site on Virulence Factor of Drug Resistant Burkholderia cenocepacia*. PMID:33769626
Estimating the Roles of Protonation and Electronic Polarization in Absolute Binding Affinity Simulations. PMID:33764050
MDock: A Suite for Molecular Inverse Docking and Target Prediction. PMID:33759135
Multiple Target Drug Design Using LigBuilder 3. PMID:33759133
From Homology Modeling to the Hit Identification and Drug Repurposing: A Structure-Based Approach in the Discovery of Novel Potential Anti-Obesity Compounds. PMID:33759132
Negative Image-Based Rescoring: Using Cavity Information to Improve Docking Screening. PMID:33759125
Negative Image-Based Screening: Rigid Docking Using Cavity Information. PMID:33759124
Simulation of Ligand Transport in Receptors Using CaverDock. PMID:33759123
Binding Mode Prediction and Virtual Screening Applications by Covalent Docking. PMID:33759121
Machine learning on ligand-residue interaction profiles to significantly improve binding affinity prediction. PMID:33758923
Ancient gene duplications in RNA viruses revealed by protein tertiary structure comparisons. PMID:33758672
Assessment of scoring functions to rank the quality of 3D subtomogram clusters from cryo-electron tomography. PMID:33753204
A small molecule compound berberine as an orally active therapeutic candidate against COVID-19 and SARS: A computational and mechanistic study. PMID:33749932
Integrating 3D structural information into systems biology. PMID:33744294
Recent advances in de novo protein design: Principles, methods, and applications. PMID:33744284
Impact of structural biologists and the Protein Data Bank on small-molecule drug discovery and development. PMID:33744282
Computational evidence for nitro derivatives of quinoline and quinoline N-oxide as low-cost alternative for the treatment of SARS-CoV-2 infection. PMID:33737545
Prioritizing antiviral drugs against SARS-CoV-2 by integrating viral complete genome sequences and drug chemical structures. PMID:33737523
EDock-ML: A web server for using ensemble docking with machine learning to aid drug discovery. PMID:33733530
α-Catenin levels determine direction of YAP/TAZ response to autophagy perturbation. PMID:33731717
Molecular storytelling for online structural biology outreach and education. PMID:33728361
Cryo-Electron Microscopy and Mass Analysis of Oligolysine-Coated DNA Nanostructures. PMID:33724780
Data mining patented antibody sequences. PMID:33722161
Vaccinomics approach for scheming potential epitope-based peptide vaccine by targeting l-protein of Marburg virus. PMID:33717824
Two Different Antibody-Dependent Enhancement (ADE) Risks for SARS-CoV-2 Antibodies. PMID:33717193
A Proteome-Wide Immunoinformatics Tool to Accelerate T-Cell Epitope Discovery and Vaccine Design in the Context of Emerging Infectious Diseases: An Ethnicity-Oriented Approach. PMID:33717077
Inhibition of interferon-stimulated gene 15 and lysine 48-linked ubiquitin binding to the SARS-CoV-2 papain-like protease by small molecules: In silico studies. PMID:33716308
A novel variant in DMXL2 gene is associated with autosomal dominant non-syndromic hearing impairment (DFNA71) in a Cameroonian family. PMID:33715530
Outliers in SAR and QSAR: 3. Importance of considering the role of water molecules in protein-ligand interactions and quantitative structure-activity relationship studies. PMID:33712973
Adapting the DeepSARM approach for dual-target ligand design. PMID:33712972
Vitamin C and Vitamin D3 show strong binding with the amyloidogenic region of G555F mutant of Fibrinogen A alpha-chain associated with renal amyloidosis: proposed possible therapeutic intervention. PMID:33710477
DNA-Directed Protein Packing within Single Crystals. PMID:33709040
Unusual RNA binding of FUS RRM studied by molecular dynamics simulation and enhanced sampling method. PMID:33705755
RNAMotifContrast: a method to discover and visualize RNA structural motif subfamilies. PMID:33693841
Accurate prediction of inter-protein residue-residue contacts for homo-oligomeric protein complexes. PMID:33693482
Complementation in trans of Porphyromonas gingivalis Lipopolysaccharide Biosynthetic Mutants Demonstrates Lipopolysaccharide Exchange. PMID:33685973
The very early evolution of protein translocation across membranes. PMID:33684113
Systematic insight into the active constituents and mechanism of Guiqi Baizhu for the treatment of gastric cancer. PMID:33682294
Mechanism of Interactions of dsDNA Binding with Apigenin and Its Sulfamate Derivatives Using Multispectroscopic, Voltammetric, and Molecular Docking Studies. PMID:33681554
Role of Phosphorylation and Hyperphosphorylation of Tau in Its Interaction with βα Dimeric Tubulin Studied from a Bioinformatics Perspective. PMID:33680370
Boulton-Katritzky Rearrangement of 5-Substituted Phenyl-3-[2-(morpholin-1-yl)ethyl]-1,2,4-oxadiazoles as a Synthetic Path to Spiropyrazoline Benzoates and Chloride with Antitubercular Properties. PMID:33673047
Zincbindpredict-Prediction of Zinc Binding Sites in Proteins. PMID:33673040
Differential Interactome Proposes Subtype-Specific Biomarkers and Potential Therapeutics in Renal Cell Carcinomas. PMID:33672271
Novel Small Molecule Hsp90/Cdc37 Interface Inhibitors Indirectly Target K-Ras-Signaling. PMID:33672199
Mechanistic Insights into Side Effects of Troglitazone and Rosiglitazone Using a Novel Inverse Molecular Docking Protocol. PMID:33670968
Heterocyclic Substitutions Greatly Improve Affinity and Stability of Folic Acid towards FRα. an In Silico Insight. PMID:33670773
Computational Selectivity Assessment of Protease Inhibitors against SARS-CoV-2. PMID:33669738
Cytotoxic Fractions from Hechtia glomerata Extracts and p-Coumaric Acid as MAPK Inhibitors. PMID:33669666
Computational Modulation of the V3 Region of Glycoprotein gp125 of HIV-2. PMID:33669351
New Mechanistic Insights on Carbon Nanotubes' Nanotoxicity Using Isolated Submitochondrial Particles, Molecular Docking, and Nano-QSTR Approaches. PMID:33668702
Computational Assessment of Chito-Oligosaccharides Interactions with Plasma Proteins. PMID:33668290
A polysaccharide utilization locus from the gut bacterium Dysgonomonas mossii encodes functionally distinct carbohydrate esterases. PMID:33667545
The active repertoire of Escherichia coli peptidoglycan amidases varies with physiochemical environment. PMID:33666292
N-Glycosylation can selectively block or foster different receptor-ligand binding modes. PMID:33664400
Potential neutralizing antibodies discovered for novel corona virus using machine learning. PMID:33664393
Loop Dynamics and Enzyme Catalysis in Protein Tyrosine Phosphatases. PMID:33661624
A comparative study of protein-ssDNA interactions. PMID:33655206
In silico screening and analysis of nonsynonymous SNPs in human CYP1A2 to assess possible associations with pathogenicity and cancer susceptibility. PMID:33654112
Androgen Receptor Binding Category Prediction with Deep Neural Networks and Structure-, Ligand-, and Statistically Based Features. PMID:33652992
Statistical Evidence for a Helical Nascent Chain. PMID:33652806
Biological impact of mutually exclusive exon switching. PMID:33651795
Rapid Identification of Inhibitors and Prediction of Ligand Selectivity for Multiple Proteins: Application to Protein Kinases. PMID:33651624
A potential peptide inhibitor of SARS-CoV-2 S and human ACE2 complex. PMID:33645443
Effect of Charge Distribution in a Modified tRNA Substrate on Pre-Reaction Protein-tRNA Complex Geometry. PMID:33644545
In silico analysis of quranic and prophetic medicinals plants for the treatment of infectious viral diseases including corona virus. PMID:33642896
Structural characterization of the self-association domain of swallow. PMID:33641207
DbStRiPs: Database of structural repeats in proteins. PMID:33641184
Structural determinants of cholesterol recognition in helical integral membrane proteins. PMID:33640379
Design of immunogens to elicit broadly neutralizing antibodies against HIV targeting the CD4 binding site. PMID:33637649
Flavonoids from Pterogyne nitens as Zika virus NS2B-NS3 protease inhibitors. PMID:33636437
Transmembrane Protein Docking with JabberDock. PMID:33635637
A Review: Molecular Chaperone-mediated Folding, Unfolding and Disaggregation of Expressed Recombinant Proteins. PMID:33634426
Utilizing Ion Mobility-Mass Spectrometry to Investigate the Unfolding Pathway of Cu/Zn Superoxide Dismutase. PMID:33634076
Therapeutic Lowering of C-Reactive Protein. PMID:33633738
A base measure of precision for protein stability predictors: structural sensitivity. PMID:33632133
Characterizing binding intensity and energetic features of histone deacetylase inhibitor pracinostat towards class I HDAC isozymes through futuristic drug designing strategy. PMID:33628709
New sulphonamide pyrolidine carboxamide derivatives: Synthesis, molecular docking, antiplasmodial and antioxidant activities. PMID:33626047
Evaluation of drug repositioning by molecular docking of pharmaceutical resources available in the Brazilian healthcare system against SARS-CoV-2. PMID:33623816
An Overview of Current Uses and Future Opportunities for Computer-Assisted Design of Vaccines for Neglected Tropical Diseases. PMID:33623396
Drug Screening of Potential Multiple Target Inhibitors for Estrogen Receptor-α-positive Breast Cancer. PMID:33622869
Inhibiting HTLV-1 Protease: A Viable Antiviral Target. PMID:33619959
Deciphering the Agonist Binding Mechanism to the Adenosine A1 Receptor. PMID:33615181
In Silico Study of Coumarins and Quinolines Derivatives as Potent Inhibitors of SARS-CoV-2 Main Protease. PMID:33614592
Flexibility and mobility of SARS-CoV-2-related protein structures. PMID:33608565
Virtual screening FDA approved drugs against multiple targets of SARS-CoV-2. PMID:33606912
Data set of competitive and allosteric protein kinase inhibitors confirmed by X-ray crystallography. PMID:33604432
Computational Prediction of Hot Spots and Binding Site of Inhibitor NSC23766 on Rac1 Binding With Tiam1. PMID:33604328
Targeting Salmonella Typhimurium Invasion and Intracellular Survival Using Pyrogallol. PMID:33603727
Enrichment analyses of diseases and pathways associated with precocious puberty using PrecocityDB. PMID:33602974
Selective inhibition of carbonic anhydrase IX and XII by coumarin and psoralen derivatives. PMID:33602041
Identification of Cryptic Binding Sites Using MixMD with Standard and Accelerated Molecular Dynamics. PMID:33599485
Structure-based peptide design targeting intrinsically disordered proteins: Novel histone H4 and H2A peptidic inhibitors. PMID:33598107
Off-target binding of an anti-amyloid beta monoclonal antibody to platelet factor 4 causes acute and chronic toxicity in cynomolgus monkeys. PMID:33596779
Mapping drug-target interactions and synergy in multi-molecular therapeutics for pressure-overload cardiac hypertrophy. PMID:33589646
Incorporating structural similarity into a scoring function to enhance the prediction of binding affinities. PMID:33588902
Epitope mimicry analysis of SARS-COV-2 surface proteins and human lung proteins. PMID:33588349
Predicting Isoform-Selective Carbonic Anhydrase Inhibitors via Machine Learning and Rationalizing Structural Features Important for Selectivity. PMID:33585783
Active Bromoaniline-Aldehyde Conjugate Systems and Their Complexes as Versatile Sensors of Multiple Cations with Logic Formulation and Efficient DNA/HSA-Binding Efficacy: Combined Experimental and Theoretical Approach. PMID:33585746
Gene Annotation in High Schools: Successful Student Pipeline and Teacher Professional Development in Bioscience Using GENI-ACT. PMID:33584559
Structural genetics of circulating variants affecting the SARS-CoV-2 spike/human ACE2 complex. PMID:33583326
Molecular docking, binding mode analysis, molecular dynamics, and prediction of ADMET/toxicity properties of selective potential antiviral agents against SARS-CoV-2 main protease: an effort toward drug repurposing to combat COVID-19. PMID:33582935
Discovery of vanoxerine dihydrochloride as a CDK2/4/6 triple-inhibitor for the treatment of human hepatocellular carcinoma. PMID:33579185
GraphBind: protein structural context embedded rules learned by hierarchical graph neural networks for recognizing nucleic-acid-binding residues. PMID:33577689
Efficient Amino Acid Conformer Search with Bayesian Optimization. PMID:33577313
Therapeutic p28 peptide targets essential H1N1 influenza virus proteins: insights from docking and molecular dynamics simulations. PMID:33575983
Diversity and evolution of bacterial bioluminescence genes in the global ocean. PMID:33575578
A Proteomic- and Bioinformatic-Based Identification of Specific Allergens from Edible Insects: Probes for Future Detection as Food Ingredients. PMID:33573235
In Silico Study of Polyunsaturated Fatty Acids as Potential SARS-CoV-2 Spike Protein Closed Conformation Stabilizers: Epidemiological and Computational Approaches. PMID:33573088
Efficient In Silico Saturation Mutagenesis of a Member of the Caspase Protease Family. PMID:33570387
Elucidating the Interactions Between Heparin/Heparan Sulfate and SARS-CoV-2-Related Proteins-An Important Strategy for Developing Novel Therapeutics for the COVID-19 Pandemic. PMID:33569392
Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). PMID:33568759
Novel Two-Component System-Like Elements Reveal Functional Domains Associated with Restriction-Modification Systems and paraMORC ATPases in Bacteria. PMID:33565597
On the Role of a Conserved Methionine in the Na+-Coupling Mechanism of a Neurotransmitter Transporter Homolog. PMID:33565025
A Three-Dimensional Model of the Yeast Transmembrane Sensor Wsc1 Obtained by SMA-Based Detergent-Free Purification and Transmission Electron Microscopy. PMID:33562593
Advances in de Novo Drug Design: From Conventional to Machine Learning Methods. PMID:33562347
Structure- and mechanism-guided design of single fluorescent protein-based biosensors. PMID:33558715
Interaction of small molecules with the SARS-CoV-2 papain-like protease: In silico studies and in vitro validation of protease activity inhibition using an enzymatic inhibition assay. PMID:33556646
Elucidation of the hetero-dimeric binding activity of LasR and RhlR proteins with the promoter DNA and the role of a specific Phe residue during the biosynthesis of HCN synthase from opportunistic pathogen Pseudomonas aeruginosa. PMID:33555486
In silico design of novel aptamers utilizing a hybrid method of machine learning and genetic algorithm. PMID:33554306
Understanding protein structural changes for oncogenic missense variants. PMID:33553733
MeCP2: The Genetic Driver of Rett Syndrome Epigenetics. PMID:33552148
RLDOCK method for predicting RNA-small molecule binding modes. PMID:33549725
Immunoinformatics Approach for the Identification and Characterization of T Cell and B Cell Epitopes towards the Peptide-Based Vaccine against SARS-CoV-2. PMID:33546870
Multiscale Simulation of Adsorption Based Microcantilever Biosensors for Radiation Exposure Effects. PMID:33542938
An expanded benchmark for antibody-antigen docking and affinity prediction reveals insights into antibody recognition determinants. PMID:33539768
Development of a Pantetheine Force Field Library for Molecular Modeling. PMID:33534558
Structural and Energetic Characterization of the Denatured State from the Perspectives of Peptides, the Coil Library, and Intrinsically Disordered Proteins. PMID:33530506
Analyzing Kinase Similarity in Small Molecule and Protein Structural Space to Explore the Limits of Multi-Target Screening. PMID:33530327
Molecular dynamics analysis of phytochemicals from Ageratina adenophora against COVID-19 main protease (Mpro) and human angiotensin-converting enzyme 2 (ACE2). PMID:33527003
Known Drugs Identified by Structure-Based Virtual Screening Are Able to Bind Sigma-1 Receptor and Increase Growth of Huntington Disease Patient-Derived Cells. PMID:33525510
REDCRAFT: A computational platform using residual dipolar coupling NMR data for determining structures of perdeuterated proteins in solution. PMID:33524015
Data-driven challenges and opportunities in crystallography. PMID:33523208
The PhoPQ Two-Component System Is the Major Regulator of Cell Surface Properties, Stress Responses and Plant-Derived Substrate Utilisation During Development of Pectobacterium versatile-Host Plant Pathosystems. PMID:33519782
Virtual screening and molecular dynamics simulation study of plant-derived compounds to identify potential inhibitors of main protease from SARS-CoV-2. PMID:33517367
Dual inhibition of SARS-CoV-2 and human rhinovirus with protease inhibitors in clinical development. PMID:33515606
Adipose saturation reduces lipotoxic systemic inflammation and explains the obesity paradox. PMID:33514548
My personal mutanome: a computational genomic medicine platform for searching network perturbing alleles linking genotype to phenotype. PMID:33514395
Hesperidin Interacts With CREB-BDNF Signaling Pathway to Suppress Pentylenetetrazole-Induced Convulsions in Zebrafish. PMID:33505312
Comparative Study of Interactions between Human cGAS and Inhibitors: Insights from Molecular Dynamics and MM/PBSA Studies. PMID:33503880
Crystal Structure of SARS-CoV-2 Main Protease in Complex with the Non-Covalent Inhibitor ML188. PMID:33503819
Bridging Themes: Short Protein Segments Found in Different Architectures. PMID:33502503
SARS-CoV-2 501Y.V2 escapes neutralization by South African COVID-19 donor plasma. PMID:33501446
Network pharmacology integrated molecular docking reveals the bioactive components and potential targets of Morinda officinalis-Lycium barbarum coupled-herbs against oligoasthenozoospermia. PMID:33500463
The Structural Properties of Odorants Modulate Their Association to Human Odorant Binding Protein. PMID:33499295
Mechanisms Applied by Protein Inhibitors to Inhibit Cysteine Proteases. PMID:33498210
A conformation-selective monoclonal antibody against a small molecule-stabilised signalling-deficient form of TNF. PMID:33495445
Structural insights into the disruption of TNF-TNFR1 signalling by small molecules stabilising a distorted TNF. PMID:33495441
Anti-Virulence Therapeutic Approaches for Neisseria gonorrhoeae. PMID:33494538
Low Basicity as a Characteristic for Atypical Ligands of Serotonin Receptor 5-HT2. PMID:33494248
On the use of 3J-coupling NMR data to derive structural information on proteins. PMID:33492494
In-depth and 3-dimensional exploration of the budding yeast phosphoproteome. PMID:33491328
Computing Cellulase Kinetics with a Two-Domain Linear Interaction Energy Approach. PMID:33490814
How Far Are We from the Rapid Prediction of Drug Resistance Arising Due to Kinase Mutations? PMID:33490784
Idarubicin-Gold Complex: From Crystal Growth to Gold Nanoparticles. PMID:33490782
Solvent Accessibility of Residues Undergoing Pathogenic Variations in Humans: From Protein Structures to Protein Sequences. PMID:33490109
NLPEI: A Novel Self-Interacting Protein Prediction Model Based on Natural Language Processing and Evolutionary Information. PMID:33488064
Residue-based pharmacophore approaches to study protein-protein interactions. PMID:33486430
Pharmacoinformatics approach based identification of potential Nsp15 endoribonuclease modulators for SARS-CoV-2 inhibition. PMID:33485847
Estimating the accuracy of pharmacophore-based detection of cognate receptor-ligand pairs in the immunoglobulin superfamily. PMID:33483991
Study of the active ingredients and mechanism of Sparganii rhizoma in gastric cancer based on HPLC-Q-TOF-MS/MS and network pharmacology. PMID:33479376
Allergen fragrance molecules: a potential relief for COVID-19. PMID:33478471
Modeling the Influenza A NP-vRNA-Polymerase Complex in Atomic Detail. PMID:33477938
Modeling the Influenza A NP-vRNA-Polymerase Complex in Atomic Detail. PMID:33477938
Prediction of Protein-ATP Binding Residues Based on Ensemble of Deep Convolutional Neural Networks and LightGBM Algorithm. PMID:33477866
Virtual Screening of Natural Compounds as Potential PI3K-AKT1 Signaling Pathway Inhibitors and Experimental Validation. PMID:33477701
Inhibition of α-, β- and γ-carbonic anhydrases from the pathogenic bacterium Vibrio cholerae with aromatic sulphonamides and clinically licenced drugs - a joint docking/molecular dynamics study. PMID:33472446
Classification and prediction of protein-protein interaction interface using machine learning algorithm. PMID:33469042
Comparative Genomics of Marine Bacteria from a Historically Defined Plastic Biodegradation Consortium with the Capacity to Biodegrade Polyhydroxyalkanoates. PMID:33467086
Identification of the Primary Factors Determining theSpecificity of Human VKORC1 Recognition by Thioredoxin-Fold Proteins. PMID:33466919
The Bile Salt Export Pump: Molecular Structure, Study Models and Small-Molecule Drugs for the Treatment of Inherited BSEP Deficiencies. PMID:33466755
Rosetta design with co-evolutionary information retains protein function. PMID:33465067
Using COVID-19 as a teaching tool in a time of remote learning: A workflow for bioinformatic approaches to identifying candidates for therapeutic and vaccine development. PMID:33463080
Structural-Genetic Characterization Of Novel Butaryl co-A Dehydrogenase and Proposition of Butanol Biosynthesis Pathway in Pusillimonas ginsengisoli SBSA. PMID:33462639
Neuropilin 1 and Neuropilin 2 gene invalidation or pharmacological inhibition reveals their relevance for the treatment of metastatic renal cell carcinoma. PMID:33461580
WIDOCK: a reactive docking protocol for virtual screening of covalent inhibitors. PMID:33458809
Network Pharmacology Approach to Explore the Potential Mechanisms of Jieduan-Niwan Formula Treating Acute-on-Chronic Liver Failure. PMID:33456481
Evolving the naturally compromised chorismate mutase from Mycobacterium tuberculosis to top performance. PMID:33453995
A deformation energy model reveals sequence-dependent property of nucleosome positioning. PMID:33452566
Comprehensive computational target fishing approach to identify Xanthorrhizol putative targets. PMID:33452398
SARS-CoV-2 infection susceptibility influenced by ACE2 genetic polymorphisms: insights from Tehran Cardio-Metabolic Genetic Study. PMID:33452303
Systematic Search for SARS-CoV-2 Main Protease Inhibitors for Drug Repurposing: Ethacrynic Acid as a Potential Drug. PMID:33451132
Theoretical Evaluation of Novel Thermolysin Inhibitors from Bacillus thermoproteolyticus. Possible Antibacterial Agents. PMID:33451037
Dynamic Network Modeling of Allosteric Interactions and Communication Pathways in the SARS-CoV-2 Spike Trimer Mutants: Differential Modulation of Conformational Landscapes and Signal Transmission via Cascades of Regulatory Switches. PMID:33448856
Virtual Screening and Design with Machine Intelligence Applied to Pim-1 Kinase Inhibitors. PMID:33448694
Characterization of sucrose non-fermenting-1 (SNF1) homologue gene in Fusarium udum WSP-V2 and its regulation by the biocontrol agent Pseudomonas fluorescens OKC. PMID:33442517
On topology and knotty entanglement in protein folding. PMID:33439862
Enfuvirtide, an HIV-1 fusion inhibitor peptide, can act as a potent SARS-CoV-2 fusion inhibitor: an in silico drug repurposing study. PMID:33438525
Prediction of kinase inhibitors binding modes with machine learning and reduced descriptor sets. PMID:33436888
Evolution of ribosomal protein network architectures. PMID:33436806
Short linear motif candidates in the cell entry system used by SARS-CoV-2 and their potential therapeutic implications. PMID:33436497
Expression, Purification and Crystallization of Asrij, A Novel Scaffold Transmembrane Protein. PMID:33433647
Visualization of very large high-dimensional data sets as minimum spanning trees. PMID:33431043
Molecular representations in AI-driven drug discovery: a review and practical guide. PMID:33431035
Identifying new topoisomerase II poison scaffolds by combining publicly available toxicity data and 2D/3D-based virtual screening. PMID:33430961
Bioactive Terpenes and Their Derivatives as Potential SARS-CoV-2 Proteases Inhibitors from Molecular Modeling Studies. PMID:33430299
Isolation, expression, and characterization of raw starch degrading α-amylase from a marine lake Bacillus megaterium NL3. PMID:33426327
Hierarchical Graph Representation of Pharmacophore Models. PMID:33425991
Secrete or perish: The role of secretion systems in Xanthomonas biology. PMID:33425257
In silico investigation on alkaloids of Rauwolfia serpentina as potential inhibitors of 3-hydroxy-3-methyl-glutaryl-CoA reductase. PMID:33424361
Genetic diversity and biological activity of Curcuma longa ecotypes from Rapa Nui using molecular markers. PMID:33424358
Human SARS CoV-2 spike protein mutations. PMID:33423311
A combined clinical and computational approach to understand the SOD1A4T-mediated pathogenesis of rapidly progressive familial amyotrophic lateral sclerosis. PMID:33420941
Exploring the Conformation and Thermal Stability of Human Serum Albumin Corona of Ferrihydrite Nanoparticles. PMID:33419335
Myricitrin, a Glycosyloxyflavone in Myrica esculenta Bark Ameliorates Diabetic Nephropathy via Improving Glycemic Status, Reducing Oxidative Stress, and Suppressing Inflammation. PMID:33419120
Structural Characterization of Act c 10.0101 and Pun g 1.0101-Allergens from the Non-Specific Lipid Transfer Protein Family. PMID:33419110
An in-silico evaluation of different bioactive molecules of tea for their inhibition potency against non structural protein-15 of SARS-CoV-2. PMID:33418408
The complexity of protein interactions unravelled from structural disorder. PMID:33417598
SoluProt: Prediction of Soluble Protein Expression in Escherichia coli. PMID:33416864
The iPPI-DB initiative: A Community-centered database of Protein-Protein Interaction modulators. PMID:33416858
Searching for potential drugs against SARS-CoV-2 through virtual screening on several molecular targets. PMID:33416020
G protein-coupled receptors: structure- and function-based drug discovery. PMID:33414387
Attenuation of Pseudomonas aeruginosa biofilm by thymoquinone: an individual and combinatorial study with tetrazine-capped silver nanoparticles and tryptophan. PMID:33411249
Crystal structure of bacterial cytotoxic necrotizing factor CNFY reveals molecular building blocks for intoxication. PMID:33410511
SialoPen peptides are new cationic foldamers with remarkable cell permeability. PMID:33409387
Clmp Regulates AMPA and Kainate Receptor Responses in the Neonatal Hippocampal CA3 and Kainate Seizure Susceptibility in Mice. PMID:33408624
Design of biologically active binary protein 2D materials. PMID:33408408
Accelerating AutoDock4 with GPUs and Gradient-Based Local Search. PMID:33403848
Anticancer Activity of Lesbicoumestan in Jurkat Cells via Inhibition of Oxidative Stress-Mediated Apoptosis and MALT1 Protease. PMID:33401649
Unpacking Pandora From Its Box: Deciphering the Molecular Basis of the SARS-CoV-2 Coronavirus. PMID:33396557
Study on the Inhibitory Activity of a Synthetic Defensin Derived from Barley Endosperm against Common Food Spoilage Yeast. PMID:33396521
Unravelling the molecular effect of ocellatin-1, F1, K1 and S1, the frog-skin antimicrobial peptides to enhance its therapeutics-quantum and molecular mechanical approaches. PMID:33392722
Evaluating Protein Transfer Learning with TAPE. PMID:33390682
Modulation of post-powerstroke dynamics in myosin II by 2'-deoxy-ADP. PMID:33388313
A Fifth of the Protein World: Rossmann-like Proteins as an Evolutionarily Successful Structural unit. PMID:33387532
Interactions between nascent proteins translated by adjacent ribosomes drive homomer assembly. PMID:33384371
Prediction of putative regulatory elements in the subgenomic promoters of cucumber green mottle mosaic virus and their interactions with the RNA dependent RNA polymerase domain. PMID:33381623
A Multi-Pronged Computational Pipeline for Prioritizing Drug Target Strategies for Latent Tuberculosis. PMID:33381491
Assessing the low complexity of protein sequences via the low complexity triangle. PMID:33378336
PremPS: Predicting the impact of missense mutations on protein stability. PMID:33378330
Caffeine and Theophylline Inhibit β-Galactosidase Activity and Reduce Expression in Escherichia coli. PMID:33376862
Deep Learning for Prediction and Optimization of Fast-Flow Peptide Synthesis. PMID:33376788
Assessment of enzyme active site positioning and tests of catalytic mechanisms through X-ray-derived conformational ensembles. PMID:33376217
Big data and artificial intelligence discover novel drugs targeting proteins without 3D structure and overcome the undruggable targets. PMID:33376199
An automated protocol for modelling peptide substrates to proteases. PMID:33375946
Alkaloids with Anti-Onchocercal Activity from Voacanga africana Stapf (Apocynaceae): Identification and Molecular Modeling. PMID:33375687
Expanding the Structural Diversity of DNA Methyltransferase Inhibitors. PMID:33375520
Disclosing the Interaction of Gold Nanoparticles with Aβ(1-40) Monomers through Replica Exchange Molecular Dynamics Simulations. PMID:33375086
Larvicidal Activity of Cinnamic Acid Derivatives: Investigating Alternative Products for Aedes aegypti L. Control. PMID:33374484
Unraveling a Force-Generating Allosteric Pathway of Actomyosin Communication Associated with ADP and Pi Release. PMID:33374308
Computational Analysis of African Swine Fever Virus Protein Space for the Design of an Epitope-Based Vaccine Ensemble. PMID:33371523
RELT stains prominently in B-cell lymphomas and binds the hematopoietic transcription factor MDFIC. PMID:33367115
An Educational Bioinformatics Project to Improve Genome Annotation. PMID:33365016
Identification of Small Molecule Inhibitors of the Deubiquitinating Activity of the SARS-CoV-2 Papain-Like Protease: in silico Molecular Docking Studies and in vitro Enzymatic Activity Assay. PMID:33364229
Protein Synthesis in the Developing Neocortex at Near-Atomic Resolution Reveals Ebp1-Mediated Neuronal Proteostasis at the 60S Tunnel Exit. PMID:33357414
Design and in silico study of the novel coumarin derivatives against SARS-CoV-2 main enzymes. PMID:33357038
Computational Insights into Allosteric Conformational Modulation of P-Glycoprotein by Substrate and Inhibitor Binding. PMID:33353070
The model structure of the hammerhead ribozyme formed by RNAs of reciprocal chirality. PMID:33351058
Essential interpretations of bioinformatics in COVID-19 pandemic. PMID:33349792
Predicting substitutions to modulate disorder and stability in coiled-coils. PMID:33349244
Explainable Deep Relational Networks for Predicting Compound-Protein Affinities and Contacts. PMID:33347301
SeSaMe: Metagenome Sequence Classification of Arbuscular Mycorrhizal Fungi-associated Microorganisms. PMID:33346086
SeSaMe PS Function: Functional Analysis of the Whole Metagenome Sequencing Data of the Arbuscular Mycorrhizal Fungi. PMID:33346085
A 10-year meta-analysis of membrane protein structural biology: Detergents, membrane mimetics, and structure determination techniques. PMID:33340490
A method for validating the accuracy of NMR protein structures. PMID:33339822
Ligand-Binding-Site Refinement to Generate Reliable Holo Protein Structure Conformations from Apo Structures. PMID:33337877
Identification of Host Cellular Protein Substrates of SARS-COV-2 Main Protease. PMID:33333742
Neuropeptide S receptor gene Asn107 polymorphism in obese male individuals in Pakistan. PMID:33332443
Probing the Dynamic Structure-Function and Structure-Free Energy Relationships of the Coronavirus Main Protease with Biodynamics Theory. PMID:33330838
Computational Modeling of NLRP3 Identifies Enhanced ATP Binding and Multimerization in Cryopyrin-Associated Periodic Syndromes. PMID:33329557
GAG-DB, the New Interface of the Three-Dimensional Landscape of Glycosaminoglycans. PMID:33322545
Immunoproteomic Analysis Reveals Novel Candidate Antigens for the Diagnosis of Paracoccidioidomycosis Due to Paracoccidioides lutzii. PMID:33322269
Interferon Beta Activity Is Modulated via Binding of Specific S100 Proteins. PMID:33322098
Propolis Suppresses UV-Induced Photoaging in Human Skin through Directly Targeting Phosphoinositide 3-Kinase. PMID:33322005
Quantification of the Resilience and Vulnerability of HIV-1 Native Glycan Shield at Atomistic Detail. PMID:33319171
Microfluidic platform enables tailored translocation and reaction cascades in nanoliter droplet networks. PMID:33318607
Structural insights and evaluation of the potential impact of missense variants on the interactions of SLIT2 with ROBO1/4 in cancer progression. PMID:33318575
Correlation of NHR-48 Transcriptional Modulator Expression with Selected CYP Genes' Expression during Thiabendazole Treatment of Anisakis simplex (s.l.)?-An In Vitro Study. PMID:33316888
Community Network Analysis of Allosteric Proteins. PMID:33315222
VIPERdb v3.0: a structure-based data analytics platform for viral capsids. PMID:33313778
Kinetic and thermodynamic analysis defines roles for two metal ions in DNA polymerase specificity and catalysis. PMID:33310704
Integrin α11β1 is a receptor for collagen XIII. PMID:33306155
Estrogen-related receptor alpha directly binds to p53 and cooperatively controls colon cancer growth through the regulation of mitochondrial biogenesis and function. PMID:33303020
Data sets on human histone interaction networks. PMID:33299912
A reference catalog of DNA palindromes in the human genome and their variations in 1000 Genomes. PMID:33298903
Scalar nanostructure of the Candida albicans cell wall; a molecular, cellular and ultrastructural analysis and interpretation. PMID:33294751
Are losartan and imatinib effective against SARS-CoV2 pathogenesis? A pathophysiologic-based in silico study. PMID:33294307
LigGrep: a tool for filtering docked poses to improve virtual-screening hit rates. PMID:33292486
Phylogenetics-based identification and characterization of a superior 2,3-butanediol dehydrogenase for Zymomonas mobilis expression. PMID:33292448
Sensing the interactions between carbohydrate-binding agents and N-linked glycans of SARS-CoV-2 spike glycoprotein using molecular docking and simulation studies. PMID:33292056
Data-guided Multi-Map variables for ensemble refinement of molecular movies. PMID:33291927
Benchmark Sets for Binding Hot Spot Identification in Fragment-Based Ligand Discovery. PMID:33291870
NKCC1, an Elusive Molecular Target in Brain Development: Making Sense of the Existing Data. PMID:33291778
Molecular Docking Simulations on Histone Deacetylases (HDAC)-1 and -2 to Investigate the Flavone Binding. PMID:33291755
Meta-analysis of viscosity of aqueous deep eutectic solvents and their components. PMID:33288787
Targeting the RdRp of Emerging RNA Viruses: The Structure-Based Drug Design Challenge. PMID:33287144
Modelling and Recognition of Protein Contact Networks by Multiple Kernel Learning and Dissimilarity Representations. PMID:33286565
Molecular Mean-Field Theory of Ionic Solutions: A Poisson-Nernst-Planck-Bikerman Model. PMID:33286322
Residue Cluster Classes: A Unified Protein Representation for Efficient Structural and Functional Classification. PMID:33286246
Design of an epitope-based peptide vaccine against the SARS-CoV-2: a vaccine-informatics approach. PMID:33285567
Identification of afzelin potential targets in inhibiting triple-negative breast cancer cell migration using reverse docking. PMID:33283065
Integrative modeling of membrane-associated protein assemblies. PMID:33277503
Revealing the structures of megadalton-scale DNA complexes with nucleotide resolution. PMID:33277481
Increased usability, algorithmic improvements and incorporation of data mining for structure calculation of proteins with REDCRAFT software package. PMID:33272215
The SPPL3-Defined Glycosphingolipid Repertoire Orchestrates HLA Class I-Mediated Immune Responses. PMID:33271119
PolyFold: An interactive visual simulator for distance-based protein folding. PMID:33270805
Benchmark of Generic Shapes for Macrocycles. PMID:33270455
Genome-wide analysis of HSP90 gene family in the Mediterranean olive (Olea europaea subsp. europaea) provides insight into structural patterns, evolution and functional diversity. PMID:33268931
Entropy and Information within Intrinsically Disordered Protein Regions. PMID:33267376
A Suggestion of Converting Protein Intrinsic Disorder to Structural Entropy Using Shannon's Information Theory. PMID:33267305
New 1,3,4-Oxadiazole Derivatives of Pyridothiazine-1,1-Dioxide with Anti-Inflammatory Activity. PMID:33266208
Deep Learning in LncRNAome: Contribution, Challenges, and Perspectives. PMID:33266128
Design, Screening, and Testing of Non-Rational Peptide Libraries with Antimicrobial Activity: In Silico and Experimental Approaches. PMID:33265897
Recifin A, Initial Example of the Tyr-Lock Peptide Structural Family, Is a Selective Allosteric Inhibitor of Tyrosyl-DNA Phosphodiesterase I. PMID:33263997
Leveraging the Entirety of the Protein Data Bank to Enable Improved Structure Prediction Based on Cross-Link Data. PMID:33263396
Identification of a Potent and Selective 5-HT1A Receptor Agonist with In Vitro and In Vivo Antinociceptive Activity. PMID:33263393
Molecular Defects in Friedreich's Ataxia: Convergence of Oxidative Stress and Cytoskeletal Abnormalities. PMID:33263002
Targeting the coronavirus SARS-CoV-2: computational insights into the mechanism of action of the protease inhibitors lopinavir, ritonavir and nelfinavir. PMID:33262359
Targeting Casein Kinase 1 (CK1) in Hematological Cancers. PMID:33261128
Screening of Human CYP1A2 and CYP3A4 Inhibitors from Seaweed In Silico and In Vitro. PMID:33260381
An in silico approach to analyze HCV genotype-specific binding-site variation and its effect on drug-protein interaction. PMID:33257748
Intermolecular Interactions in Crystal Structures of Imatinib-Containing Compounds. PMID:33255944
Are Dietary Lectins Relevant Allergens in Plant Food Allergy? PMID:33255208
Schistosoma mansoni venom allergen-like protein 6 (SmVAL6) maintains tegumental barrier function. PMID:33253697
A multiscale coarse-grained model of the SARS-CoV-2 virion. PMID:33253634
Combination of QSAR, molecular docking, molecular dynamic simulation and MM-PBSA: analogues of lopinavir and favipiravir as potential drug candidates against COVID-19. PMID:33251975
Structure-based drug designing of naphthalene based SARS-CoV PLpro inhibitors for the treatment of COVID-19. PMID:33251371
A conserved multi-epitope-based vaccine designed by targeting hemagglutinin protein of highly pathogenic avian H5 influenza viruses. PMID:33251084
NOTCH1: Review of its role in lymphatic development and study of seven families with rare pathogenic variants. PMID:33247628
Licochalcone A inhibits EGFR signalling and translationally suppresses survivin expression in human cancer cells. PMID:33247550
Identification of the anti-breast cancer targets of triterpenoids in Liquidambaris Fructus and the hints for its traditional applications. PMID:33246450
MarkerDB: an online database of molecular biomarkers. PMID:33245771
Excavating the functionally crucial active-site residues of the DXS protein of Bacillus subtilis by exploring its closest homologues. PMID:33242110
Contributions of protein microenvironment in tannase industrial applicability: An in-silico comparative study of pathogenic and non-pathogenic bacterial tannase. PMID:33241136
Properties of Cavities in Biological Structures-A Survey of the Protein Data Bank. PMID:33240933
Identification of L-asparaginases from Streptomyces strains with competitive activity and immunogenic profiles: a bioinformatic approach. PMID:33240625
Identification of Novel BRCA1 and RAD50 Mutations Associated With Breast Cancer Predisposition in Tunisian Patients. PMID:33240314
A Functional Kinase Is Necessary for Cyclin-Dependent Kinase G1 (CDKG1) to Maintain Fertility at High Ambient Temperature in Arabidopsis. PMID:33240303
Structural Modeling and Molecular Dynamics of the Immune Checkpoint Molecule HLA-G. PMID:33240264
Anti-Quorum Sensing Activity of Stevia Extract, Stevioside, Rebaudioside A and Their Aglycon Steviol. PMID:33238612
Phosphoglycerate kinase: structural aspects and functions, with special emphasis on the enzyme from Kinetoplastea. PMID:33234025
Repositioned Drugs for Chagas Disease Unveiled via Structure-Based Drug Repositioning. PMID:33233837
Synthesis of Palladium(II) Complexes via Michael Addition: Antiproliferative Effects through ROS-Mediated Mitochondrial Apoptosis and Docking with SARS-CoV-2. PMID:33231439
Bioengineering of non-pathogenic Escherichia coli to enrich for accumulation of environmental copper. PMID:33230130
A cassava protoplast system for screening genes associated with the response to South African cassava mosaic virus. PMID:33228712
Structural bioinformatics enhances mechanistic interpretation of genomic variation, demonstrated through the analyses of 935 distinct RAS family mutations. PMID:33226070
The urgent need for pan-antiviral agents: from multitarget discovery to multiscale design. PMID:33225723
Effect of pH on the Ability of N-Terminal Domain of Human NPC1 to Recognize, Bind, and Transfer Cholesterol. PMID:33225153
Structural Analysis of (p)ppGpp Reveals Its Versatile Binding Pattern for Diverse Types of Target Proteins. PMID:33224117
The UCSC Genome Browser database: 2021 update. PMID:33221922
Genetic analysis of SARS-CoV-2 isolates collected from Bangladesh: Insights into the origin, mutational spectrum and possible pathomechanism. PMID:33221119
Conformational Ensembles of Antibodies Determine Their Hydrophobicity. PMID:33220303
Prediction of Burkholderia pseudomallei DsbA substrates identifies potential virulence factors and vaccine targets. PMID:33216758
Pangenome Analysis of Mycobacterium tuberculosis Reveals Core-Drug Targets and Screening of Promising Lead Compounds for Drug Discovery. PMID:33213029
Segregation Analysis of Rare NRP1 and NRP2 Variants in Families with Lymphedema. PMID:33212964
RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences. PMID:33211854
qFit 3: Protein and ligand multiconformer modeling for X-ray crystallographic and single-particle cryo-EM density maps. PMID:33210433
Current Challenges and Opportunities in Designing Protein-Protein Interaction Targeted Drugs. PMID:33209039
Structure and function of virion RNA polymerase of a crAss-like phage. PMID:33208949
BioAFMviewer: An interactive interface for simulated AFM scanning of biomolecular structures and dynamics. PMID:33206646
Accounting for the Central Role of Interfacial Water in Protein-Ligand Binding Free Energy Calculations. PMID:33206520
In vitro and in silico studies of 8(17),12E,14-labdatrien-18-oic acid in airways smooth muscle relaxation: new molecular insights about its mechanism of action. PMID:33205250
Staphylococcal DNA Repair Is Required for Infection. PMID:33203752
A Geometric Definition of Short to Medium Range Hydrogen-Mediated Interactions in Proteins. PMID:33203097
Genetic Adaptation of Coxsackievirus B1 during Persistent Infection in Pancreatic Cells. PMID:33203081
Automated, Accurate, and Scalable Relative Protein-Ligand Binding Free-Energy Calculations Using Lambda Dynamics. PMID:33201701
A multiple peptides vaccine against COVID-19 designed from the nucleocapsid phosphoprotein (N) and Spike Glycoprotein (S) via the immunoinformatics approach. PMID:33200089
Investigation of the Effect of Temperature on the Structure of SARS-CoV-2 Spike Protein by Molecular Dynamics Simulations. PMID:33195427
Mechanisms of Core Chinese Herbs against Colorectal Cancer: A Study Based on Data Mining and Network Pharmacology. PMID:33193800
Identifying Effective Antiviral Drugs Against SARS-CoV-2 by Drug Repositioning Through Virus-Drug Association Prediction. PMID:33193695
Advances in RNA 3D Structure Modeling Using Experimental Data. PMID:33193680
In and Outs of Chuviridae Endogenous Viral Elements: Origin of a Potentially New Retrovirus and Signature of Ancient and Ongoing Arms Race in Mosquito Genomes. PMID:33193616
Predicting Cross-Reactivity and Antigen Specificity of T Cell Receptors. PMID:33193332
In vitro and in silico evaluation of the inhibitory effect of a curcumin-based oxovanadium (IV) complex on alkaline phosphatase activity and bacterial biofilm formation. PMID:33191462
Conserved patterns and interactions in the unfolding transition state across SH3 domain structural homologues. PMID:33190305
Culinary spice bioactives as potential therapeutics against SARS-CoV-2: Computational investigation. PMID:33190011
Virus Isoelectric Point Estimation: Theories and Methods. PMID:33188001
RCSB Protein Data Bank: Architectural Advances Towards Integrated Searching and Efficient Access to Macromolecular Structure Data from the PDB Archive. PMID:33186584
Molecular docking simulation reveals ACE2 polymorphisms that may increase the affinity of ACE2 with the SARS-CoV-2 Spike protein. PMID:33181224
Ground-State Destabilization by Active-Site Hydrophobicity Controls the Selectivity of a Cofactor-Free Decarboxylase. PMID:33180505
Few-shot learning for classification of novel macromolecular structures in cryo-electron tomograms. PMID:33175839
Association of the DNASE1L3 rs35677470 polymorphism with systemic lupus erythematosus, rheumatoid arthritis and systemic sclerosis: Structural biological insights. PMID:33173951
Biological network analysis with deep learning. PMID:33169146
Insightful Valorization of the Biological Activities of Pani Heloch Leaves through Experimental and Computer-Aided Mechanisms. PMID:33167510
Comparative Analysis of Nanomechanical Features of Coronavirus Spike Proteins and Correlation with Lethality and Infection Rate. PMID:33163958
Computational drug re-purposing targeting the spike glycoprotein of SARS-CoV-2 as an effective strategy to neutralize COVID-19. PMID:33160938
Coevolution, Dynamics and Allostery Conspire in Shaping Cooperative Binding and Signal Transmission of the SARS-CoV-2 Spike Protein with Human Angiotensin-Converting Enzyme 2. PMID:33158276
A Small Molecule that Binds an RNA Repeat Expansion Stimulates Its Decay via the Exosome Complex. PMID:33157036
TCRD and Pharos 2021: mining the human proteome for disease biology. PMID:33156327
On the Use of Side-Chain NMR Relaxation Data to Derive Structural and Dynamical Information on Proteins: A Case Study Using Hen Lysozyme. PMID:33146424
Pathway enrichment analysis of virus-host interactome and prioritization of novel compounds targeting the spike glycoprotein receptor binding domain-human angiotensin-converting enzyme 2 interface to combat SARS-CoV-2. PMID:33146070
CYP154C5 Regioselectivity in Steroid Hydroxylation Explored by Substrate Modifications and Protein Engineering*. PMID:33145893
Simplified geometric representations of protein structures identify complementary interaction interfaces. PMID:33140424
Man-Specific, GalNAc/T/Tn-Specific and Neu5Ac-Specific Seaweed Lectins as Glycan Probes for the SARS-CoV-2 (COVID-19) Coronavirus. PMID:33138151
Alpha-Carbonic Anhydrases from Hydrothermal Vent Sources as Potential Carbon Dioxide Sequestration Agents: In Silico Sequence, Structure and Dynamics Analyses. PMID:33138066
Cornus officinalis Ethanolic Extract with Potential Anti-Allergic, Anti-Inflammatory, and Antioxidant Activities. PMID:33138027
Interaction of small molecules with the SARS-CoV-2 main protease in silico and in vitro validation of potential lead compounds using an enzyme-linked immunosorbent assay. PMID:33137690
Human coronavirus spike protein-host receptor recognition. PMID:33137344
RNA inter-nucleotide 3D closeness prediction by deep residual neural networks. PMID:33135062
Trametinib Induces the Stabilization of a Dual GNAQ p.Gly48Leu- and FGFR4 p.Cys172Gly-Mutated Uveal Melanoma. The Role of Molecular Modelling in Personalized Oncology. PMID:33126538
RNA structure prediction using positive and negative evolutionary information. PMID:33125376
Synthesis and evaluation of anticancer activities of 2- or 4-substituted 3-(N-benzyltriazolylmethyl)-13α-oestrone derivatives. PMID:33121276
The MemMoRF database for recognizing disordered protein regions interacting with cellular membranes. PMID:33119751
GridSolvate: A Web Server for the Prediction of Biomolecular Hydration Properties. PMID:33119305
HT-SuMD: making molecular dynamics simulations suitable for fragment-based screening. A comparative study with NMR. PMID:33115279
Critical Sequence Hotspots for Binding of Novel Coronavirus to Angiotensin Converter Enzyme as Evaluated by Molecular Simulations. PMID:33112147
Pleiotropic roles of cold shock proteins with special emphasis on unexplored cold shock protein member of Plasmodium falciparum. PMID:33109193
Discovery of small molecule PLpro inhibitor against COVID-19 using structure-based virtual screening, molecular dynamics simulation, and molecular mechanics/Generalized Born surface area (MM/GBSA) calculation. PMID:33106741
DrugSpaceX: a large screenable and synthetically tractable database extending drug space. PMID:33104791
Hybrid MM/CG Webserver: Automatic Set Up of Molecular Mechanics/Coarse-Grained Simulations for Human G Protein-Coupled Receptor/Ligand Complexes. PMID:33102525
Identification of histone deacetylase inhibitors with (arylidene)aminoxy scaffold active in uveal melanoma cell lines. PMID:33100043
Identification of Putative Non-Substrate-Based XT-I Inhibitors by Natural Product Library Screening. PMID:33096778
RLDOCK: A New Method for Predicting RNA-Ligand Interactions. PMID:33095555
Adeno-Associated Virus (AAV-DJ)-Cryo-EM Structure at 1.56 Å Resolution. PMID:33092282
Edge Strand Dissociation and Conformational Changes in Transthyretin under Amyloidogenic Conditions. PMID:33091379
Data set of activity cliffs with single-atom modification and associated X-ray structure information for medicinal and computational chemistry applications. PMID:33088875
In silico assessment of natural products and approved drugs as potential inhibitory scaffolds targeting aminoacyl-tRNA synthetases from Plasmodium. PMID:33088666
DNA mismatches reveal conformational penalties in protein-DNA recognition. PMID:33087930
Structural and functional characterization of G protein-coupled receptors with deep mutational scanning. PMID:33084570
Computational tools for drawing, building and displaying carbohydrates: a visual guide. PMID:33082879
Large-scale in silico mutagenesis experiments reveal optimization of genetic code and codon usage for protein mutational robustness. PMID:33081759
Performance of Force-Field- and Machine Learning-Based Scoring Functions in Ranking MAO-B Protein-Inhibitor Complexes in Relevance to Developing Parkinson's Therapeutics. PMID:33081086
SARS-CoV-2 Disrupts Splicing, Translation, and Protein Trafficking to Suppress Host Defenses. PMID:33080218
The Dark Kinase Knowledgebase: an online compendium of knowledge and experimental results of understudied kinases. PMID:33079988
Downhill, Ultrafast and Fast Folding Proteins Revised. PMID:33076540
Structural and molecular basis of the interaction mechanism of selected drugs towards multiple targets of SARS-CoV-2 by molecular docking and dynamic simulation studies- deciphering the scope of repurposed drugs. PMID:33074111
Structural basis for the inhibition of SARS-CoV2 main protease by Indian medicinal plant-derived antiviral compounds. PMID:33073712
Protein structure, amino acid composition and sequence determine proteome vulnerability to oxidation-induced damage. PMID:33073387
Down-regulation of COX-2 activity by 1α,25(OH)2D3 is VDR dependent in endothelial cells transformed by Kaposi's sarcoma-associated herpesvirus G protein-coupled receptor. PMID:33072916
The discovery of novel antitrypanosomal 4-phenyl-6-(pyridin-3-yl)pyrimidines. PMID:33070078
Structure-based design and discovery of novel anti-tissue factor antibodies with cooperative double-point mutations, using interaction analysis. PMID:33067496
Synergistic Cytotoxic Effect from Combination of Wedelolactone and Cisplatin in HeLa Cell Line: A Novel Finding. PMID:33061291
Papain-like cysteine proteinase zone (PCP-zone) and PCP structural catalytic core (PCP-SCC) of enzymes with cysteine proteinase fold. PMID:33058970
ProteinUnet-An efficient alternative to SPIDER3-single for sequence-based prediction of protein secondary structures. PMID:33058261
Sensory Perception of Non-Deuterated and Deuterated Organic Compounds. PMID:33058253
Molecular Modeling of µ Opioid Receptor Ligands with Various Functional Properties: PZM21, SR-17018, Morphine, and Fentanyl-Simulated Interaction Patterns Confronted with Experimental Data. PMID:33053718
A Sweep of Earth's Virome Reveals Host-Guided Viral Protein Structural Mimicry and Points to Determinants of Human Disease. PMID:33053371
DNAmoreDB, a database of DNAzymes. PMID:33053178
Virus database annotations assist in tracing information on patients infected with emerging pathogens. PMID:33052312
Comparative docking studies to understand the binding affinity of nicotine with soluble ACE2 (sACE2)-SARS-CoV-2 complex over sACE2. PMID:33052306
MCCS, a novel characterization method for protein-ligand complex. PMID:33051641
Structural and Computational Insights into a Blebbistatin-Bound Myosin•ADP Complex with Characteristics of an ADP-Release Conformation along the Two-Step Myosin Power Stoke. PMID:33049993
Drug binding dynamics of the dimeric SARS-CoV-2 main protease, determined by molecular dynamics simulation. PMID:33046764
Assessing multiple score functions in Rosetta for drug discovery. PMID:33044994
Modeling the Role of a Flexible Loop and Active Site Side Chains in Hydride Transfer Catalyzed by Glycerol-3-phosphate Dehydrogenase. PMID:33042609
Integrating Machine Learning-Based Virtual Screening With Multiple Protein Structures and Bio-Assay Evaluation for Discovery of Novel GSK3β Inhibitors. PMID:33041806
Resveratrol suppresses the growth and metastatic potential of cervical cancer by inhibiting STAT3Tyr705 phosphorylation. PMID:33040485
Immunoinformatics approach to understand molecular interaction between multi-epitopic regions of SARS-CoV-2 spike-protein with TLR4/MD-2 complex. PMID:33039603
Steered molecular dynamic simulations reveal Marfan syndrome mutations disrupt fibrillin-1 cbEGF domain mechanosensitive calcium binding. PMID:33033378
De novo missense variants disrupting protein-protein interactions affect risk for autism through gene co-expression and protein networks in neuronal cell types. PMID:33032641
Investigating Potential Inhibitory Effect of Uncaria tomentosa (Cat's Claw) against the Main Protease 3CLpro of SARS-CoV-2 by Molecular Modeling. PMID:33029165
Amyloid precursor protein is a restriction factor that protects against Zika virus infection in mammalian brains. PMID:33028637
Molecular evolutionary and structural analysis of human UCHL1 gene demonstrates the relevant role of intragenic epistasis in Parkinson's disease and other neurological disorders. PMID:33028204
1,2,4 triazolo[1,5-a] pyrimidin-7-ones as novel SARS-CoV-2 Main protease inhibitors: In silico screening and molecular dynamics simulation of potential COVID-19 drug candidates. PMID:33022567
Kinetic characterization and structure analysis of an altered polyol dehydrogenase with d-lactate dehydrogenase activity. PMID:33020946
In Silico Prediction of Protein Adsorption Energy on Titanium Dioxide and Gold Nanoparticles. PMID:33020391
Antigenic and Substrate Preference Differences between Scorpion and Spider Dermonecrotic Toxins, a Comparative Investigation. PMID:33019554
Network theory of the bacterial ribosome. PMID:33017414
Structural analysis, virtual screening and molecular simulation to identify potential inhibitors targeting 2'-O-ribose methyltransferase of SARS-CoV-2 coronavirus. PMID:33016237
A database resource and online analysis tools for coronaviruses on a historical and global scale. PMID:33009914
Deep phylogeny of cancer drivers and compensatory mutations. PMID:33009502
Structural diversity and phylogenetic distribution of valyl tRNA-like structures in viruses. PMID:33008837
Kojic acid repurposing as a pancreatic lipase inhibitor and the optimization of its production from a local Aspergillus oryzae soil isolate. PMID:33008398
The Inhibitory Effect of Extra Virgin Olive Oil and Its Active Compound Oleocanthal on Prostaglandin-Induced Uterine Hypercontraction and Pain-Ex Vivo and In Vivo Study. PMID:33008039
A Novel Series of [1,2,4]Triazolo[4,3-a]Pyridine Sulfonamides as Potential Antimalarial Agents: In Silico Studies, Synthesis and In Vitro Evaluation. PMID:33007887
Molecular Simulations and Network Modeling Reveal an Allosteric Signaling in the SARS-CoV-2 Spike Proteins. PMID:33006900
Recent advances on the machine learning methods in predicting ncRNA-protein interactions. PMID:33006667
Synthesis, molecular docking, antiplasmodial and antioxidant activities of new sulfonamido-pepetide derivatives. PMID:33005786
enAsCas12a Enables CRISPR-Directed Evolution to Screen for Functional Drug Resistance Mutations in Sequences Inaccessible to SpCas9. PMID:33002419
In-silico design of a potential inhibitor of SARS-CoV-2 S protein. PMID:33002032
Repurposing Benzbromarone for Familial Amyloid Polyneuropathy: A New Transthyretin Tetramer Stabilizer. PMID:32998442
The First Berberine-Based Inhibitors of Tyrosyl-DNA Phosphodiesterase 1 (Tdp1), an Important DNA Repair Enzyme. PMID:32998385
Computational and In Vitro Investigation of (-)-Epicatechin and Proanthocyanidin B2 as Inhibitors of Human Matrix Metalloproteinase 1. PMID:32998374
Inhibitory Potential of Polyclonal Camel Antibodies against New Delhi Metallo-β-lactamase-1 (NDM-1). PMID:32998307
IDPology of the living cell: intrinsic disorder in the subcellular compartments of the human cell. PMID:32997198
Protein profiles: Biases and protocols. PMID:32994887
Comparative molecular docking analysis of the SARS CoV-2 Spike glycoprotein with the human ACE-2 receptors and thrombin. PMID:32994678
Streamlined and Abundant Bacterioplankton Thrive in Functional Cohorts. PMID:32994284
How Does Replacement of the Axial Histidine Ligand in Cytochrome c Peroxidase by Nδ-Methyl Histidine Affect Its Properties and Functions? A Computational Study. PMID:32992593
Focus on Human Monoamine Transporter Selectivity. New Human DAT and NET Models, Experimental Validation, and SERT Affinity Exploration. PMID:32991141
Mouse Models of Human Pathogenic Variants of TBC1D24 Associated with Non-Syndromic Deafness DFNB86 and DFNA65 and Syndromes Involving Deafness. PMID:32987832
A nonsense variant in Rap Guanine Nucleotide Exchange Factor 5 (RAPGEF5) is associated with equine familial isolated hypoparathyroidism in Thoroughbred foals. PMID:32986719
Pyrrolo[2',3':3,4]cyclohepta[1,2-d][1,2]oxazoles, a New Class of Antimitotic Agents Active against Multiple Malignant Cell Types. PMID:32986419
Predicting binding sites from unbound versus bound protein structures. PMID:32985584
A Network Pharmacological Approach to Investigate the Mechanism of Action of Active Ingredients of Epimedii Herba and Their Potential Targets in Treatment of Alzheimer's Disease. PMID:32980851
Identification and characterization of deschloro-chlorothricin obtained from a large natural product library targeting aurora A kinase in multiple myeloma. PMID:32978717
Improved Virus Isoelectric Point Estimation by Exclusion of Known and Predicted Genome-Binding Regions. PMID:32978129
Syk Inhibitors: New Computational Insights into Their Intraerythrocytic Action in Plasmodium falciparum Malaria. PMID:32977621
DIGGER: exploring the functional role of alternative splicing in protein interactions. PMID:32976589
Uncovering protein structure. PMID:32975287
Evolutionary history of dimethylsulfoniopropionate (DMSP) demethylation enzyme DmdA in marine bacteria. PMID:32974097
Molecular basis for a new bovine model of Niemann-Pick type C disease. PMID:32970694
The origin of the high stability of 3'-terminal uridine tetrads: contributions of hydrogen bonding, stacking interactions, and steric factors evaluated using modified oligonucleotide analogs. PMID:32967936
Antiallodynic effect of PhAR-DBH-Me involves cannabinoid and TRPV1 receptors. PMID:32965798
Repurposing drugs for treatment of SARS-CoV-2 infection: computational design insights into mechanisms of action. PMID:32964805
Innovations in CAZyme gene diversity and its modification for biorefinery applications. PMID:32963975
Discovery of Novel Hsp90 C-Terminal Inhibitors Using 3D-Pharmacophores Derived from Molecular Dynamics Simulations. PMID:32962253
Comprehensive Survey and Comparative Assessment of RNA-Binding Residue Predictions with Analysis by RNA Type. PMID:32961749
Targeting Multiple Binding Sites on Cholera Toxin B with Glycomimetic Polymers Promotes the Formation of Protein-Polymer Aggregates. PMID:32960582
Theoretical Insights into the Anti-SARS-CoV-2 Activity of Chloroquine and Its Analogs and In Silico Screening of Main Protease Inhibitors. PMID:32960061
Structural Heterogeneities of the Ribosome: New Frontiers and Opportunities for Cryo-EM. PMID:32957592
Impact of missense mutations in the ALDH7A1 gene on enzyme structure and catalytic function. PMID:32956737
Extension of the taxonomic coverage of the family GH126 outside Firmicutes and in silico characterization of its non-catalytic terminal domains. PMID:32953382
Piezo1 Forms Specific, Functionally Important Interactions with Phosphoinositides and Cholesterol. PMID:32949489
Five Novel Non-Sialic Acid-Like Scaffolds Inhibit In Vitro H1N1 and H5N2 Neuraminidase Activity of Influenza a Virus. PMID:32947893
An Investigation of Three-Finger Toxin-nAChR Interactions through Rosetta Protein Docking. PMID:32947868
TIE1 as a Candidate Gene for Lymphatic Malformations with or without Lymphedema. PMID:32947856
Methylation of Methyl 4-Hydroxy-2-thioxo-1,2-dihydroquinoline-3-carboxylate: Synthetic, Crystallographic, and Molecular Docking Studies. PMID:32947763
Structural Insights into the Binding Modes of Viral RNA-Dependent RNA Polymerases Using a Function-Site Interaction Fingerprint Method for RNA Virus Drug Discovery. PMID:32946692
Substrate-Dependent Modulation of SIRT2 by a Fluorescent Probe, 1-Aminoanthracene. PMID:32941003
The susceptibility of disulfide bonds towards radiation damage may be explained by S⋯O interactions. PMID:32939274
RCSB Protein Data Bank tools for 3D structure-guided cancer research: human papillomavirus (HPV) case study. PMID:32939013
Structure of Cytochrome P450 2C9*2 in Complex with Losartan: Insights into the Effect of Genetic Polymorphism. PMID:32938720
Computationally identifying hot spots in protein-DNA binding interfaces using an ensemble approach. PMID:32938375
The CASP13-CAPRI targets as case studies to illustrate a novel scoring pipeline integrating CONSRANK with clustering and interface analyses. PMID:32938371
Morphing of Amphipathic Helices to Explore the Activity and Selectivity of Membranolytic Antimicrobial Peptides. PMID:32936629
Personalized Medicine Using Cutting Edge Technologies for Genetic Epilepsies. PMID:32933463
Synthesis of 1,2,3-triazolyl nucleoside analogues and their antiviral activity. PMID:32930935
Origin-independent analysis links SARS-CoV-2 local genomes with COVID-19 incidence and mortality. PMID:32924062
Research on the potential mechanism of Chuanxiong Rhizoma on treating Diabetic Nephropathy based on network pharmacology. PMID:32922187
Atypical immune phenotype in severe combined immunodeficiency patients with novel mutations in IL2RG and JAK3. PMID:32921793
A graph-based approach identifies dynamic H-bond communication networks in spike protein S of SARS-CoV-2. PMID:32919067
Chemical shifts-based similarity restraints improve accuracy of RNA structures determined via NMR. PMID:32917774
The Active Compounds and Therapeutic Mechanisms of Pentaherbs Formula for Oral and Topical Treatment of Atopic Dermatitis Based on Network Pharmacology. PMID:32916837
Unlocking COVID therapeutic targets: A structure-based rationale against SARS-CoV-2, SARS-CoV and MERS-CoV Spike. PMID:32913581
Halogen-Bonded Guanine Base Pairs, Quartets and Ribbons. PMID:32911856
Mutations in the ARAP3 Gene in Three Families with Primary Lymphedema Negative for Mutations in Known Lymphedema-Associated Genes. PMID:32908855
A unified framework for packing deformable and non-deformable subcellular structures in crowded cryo-electron tomogram simulation. PMID:32907544
Repurposing of FDA-Approved Toremifene to Treat COVID-19 by Blocking the Spike Glycoprotein and NSP14 of SARS-CoV-2. PMID:32907334
Comparative Analysis of Bacteriophytochrome Agp2 and Its Engineered Photoactivatable NIR Fluorescent Proteins PAiRFP1 and PAiRFP2. PMID:32906690
Natural Products Impacting DNA Methyltransferases and Histone Deacetylases. PMID:32903500
How bioinformatics resources work with G4 RNAs. PMID:32898859
Azole derivatives with naphthalene showing potent antifungal effects against planktonic and biofilm forms of Candida spp.: an in vitro and in silico study. PMID:32889579
Catch and Anchor Approach To Combat Both Toxicity and Longevity of Botulinum Toxin A. PMID:32886509
UCSF ChimeraX: Structure visualization for researchers, educators, and developers. PMID:32881101
Immunoglobulins or Antibodies: IMGT® Bridging Genes, Structures and Functions. PMID:32878258
Towards the automation of in situ experimental phasing. PMID:32876055
Molecular-Level Understanding of the Somatostatin Receptor 1 (SSTR1)-Ligand Binding: A Structural Biology Study Based on Computational Methods. PMID:32875251
Automatic Identification of Players in the Flavonoid Biosynthesis with Application on the Biomedicinal Plant Croton tiglium. PMID:32867203
Molecular dynamics simulation of docking structures of SARS-CoV-2 main protease and HIV protease inhibitors. PMID:32863430
A De novo Peptide from a High Throughput Peptide Library Blocks Myosin A -MTIP Complex Formation in Plasmodium falciparum. PMID:32859024
Effect of Protein Structure on Evolution of Cotranslational Folding. PMID:32857962
Epidemiologic, Phenotypic, and Structural Characterization of Aminoglycoside-Resistance Gene aac(3)-IV. PMID:32854436
The Voltage-Dependent Deactivation of the KvAP Channel Involves the Breakage of Its S4 Helix. PMID:32850956
Enhancing intracellular accumulation and target engagement of PROTACs with reversible covalent chemistry. PMID:32848159
PSCAN: Spatial scan tests guided by protein structures improve complex disease gene discovery and signal variant detection. PMID:32847609
Biosensing Cytokine IL-6: A Comparative Analysis of Natural and Synthetic Receptors. PMID:32847008
Identification of the Effects of Aspirin and Sulindac Sulfide on the Inhibition of HMGA2-Mediated Oncogenic Capacities in Colorectal Cancer. PMID:32842685
Elucidating the Inhibitory Effect of Resveratrol and Its Structural Analogs on Selected Nucleotide-Related Enzymes. PMID:32842666
Viroinformatics approach to explore the inhibitory mechanism of existing drugs repurposed to fight against COVID-19. PMID:32841640
Diversity and classification of cyclic-oligonucleotide-based anti-phage signalling systems. PMID:32839535
SARS-CoV-2, an evolutionary perspective of interaction with human ACE2 reveals undiscovered amino acids necessary for complex stability. PMID:32837536
Repurposing metocurine as main protease inhibitor to develop novel antiviral therapy for COVID-19. PMID:32837119
Predicted therapeutic targets for COVID-19 disease by inhibiting SARS-CoV-2 and its related receptors. PMID:32835083
Die Coronavirus Structural Task Force. PMID:32834542
COVID-19 and SARS-CoV-2. Modeling the present, looking at the future. PMID:32834430
Design, Synthesis, and Biological Evaluation of Novel 7H-[1,2,4]Triazolo[3,4-b][1,3,4]thiadiazine Inhibitors as Antitumor Agents. PMID:32832771
Analysis of the vibrational and sound spectrum of over 100,000 protein structures and application in sonification. PMID:32832588
Computational-based insights into the phylogeny, structure, and function of Rhodococcus alkane-1-monooxygenase. PMID:32832341
Enhancing a de novo enzyme activity by computationally-focused ultra-low-throughput screening. PMID:32832059
Structural analysis of experimental drugs binding to the SARS-CoV-2 target TMPRSS2. PMID:32829149
How Do Molecular Dynamics Data Complement Static Structural Data of GPCRs. PMID:32824756
Putative SARS-CoV-2 Mpro Inhibitors from an In-House Library of Natural and Nature-Inspired Products: A Virtual Screening and Molecular Docking Study. PMID:32824454
The Role of APOSTART in Switching between Sexuality and Apomixis in Poa pratensis. PMID:32824095
Nicotinic Cholinergic System and COVID-19: In Silico Identification of an Interaction between SARS-CoV-2 and Nicotinic Receptors with Potential Therapeutic Targeting Implications. PMID:32823591
Characterization of the Corynebacterium glutamicum dehydroshikimate dehydratase QsuB and its potential for microbial production of protocatechuic acid. PMID:32822353
Genomic and transcriptomic insights into Raffaelea lauricola pathogenesis. PMID:32819276
Docking-based virtual screening of TβR1 inhibitors: evaluation of pose prediction and scoring functions. PMID:32818203
Complete Genome Sequence of Sulfitobacter Phage ϕGT1, Isolated from a Tidal Flat. PMID:32817157
Regulatory effects of post-translational modifications on zDHHC S-acyltransferases. PMID:32817054
FuSe: a tool to move RNA-Seq analyses from chromosomal/gene loci to functional grouping of mRNA transcripts. PMID:32814975
Nearest-neighbor amino acids of specificity-determining residues influence the activity of engineered Cre-type recombinases. PMID:32814809
Catalytic Mechanism of Aromatic Nitration by Cytochrome P450 TxtE: Involvement of a Ferric-Peroxynitrite Intermediate. PMID:32811149
Improvement of cryo-EM maps by density modification. PMID:32807957
A Hybrid Levenberg-Marquardt Algorithm on a Recursive Neural Network for Scoring Protein Models. PMID:32804373
Global alignment and assessment of TRP channel transmembrane domain structures to explore functional mechanisms. PMID:32804077
Purinergic Signaling: Impact of GPCR Structures on Rational Drug Design. PMID:32803849
Virtual Boot Camp: COVID-19 evolution and structural biology. PMID:32797732
Unsupervised protein embeddings outperform hand-crafted sequence and structure features at predicting molecular function. PMID:32797179
Parallel Discovery Strategies Provide a Basis for Riboswitch Ligand Design. PMID:32795418
Identification of peptides interfering with the LRRK2/PP1 interaction. PMID:32790695
Probing conformational transitions towards mutagenic Watson-Crick-like G·T mismatches using off-resonance sugar carbon R1ρ relaxation dispersion. PMID:32789613
Computational analysis of complement inhibitor compstatin using molecular dynamics. PMID:32789582
Structure of the essential inner membrane lipopolysaccharide-PbgA complex. PMID:32788728
Prediction and evaluation of deleterious and disease causing non-synonymous SNPs (nsSNPs) in human NF2 gene responsible for neurofibromatosis type 2 (NF2). PMID:32787631
Interaction of Drug Candidates with Various SARS-CoV-2 Receptors: An in Silico Study to Combat COVID-19. PMID:32786890
Alignment-Integrated Reconstruction of Ancestral Sequences Improves Accuracy. PMID:32785673
A chemical interpretation of protein electron density maps in the worldwide protein data bank. PMID:32785279
Antimicrobial Peptide TP4 Targets Mitochondrial Adenine Nucleotide Translocator 2. PMID:32784874
Removal of N-linked glycans in cellobiohydrolase Cel7A from Trichoderma reesei reveals higher activity and binding affinity on crystalline cellulose. PMID:32782472
In Silico Investigation of First-Pass Effect on Selected Small Molecule Excipients and Structural Dynamics of P-glycoprotein. PMID:32782427
ResiRole: residue-level functional site predictions to gauge the accuracies of protein structure prediction techniques. PMID:32780798
A Searchable Database of Crystallization Cocktails in the PDB: Analyzing the Chemical Condition Space. PMID:32776019
Repurposing of known anti-virals as potential inhibitors for SARS-CoV-2 main protease using molecular docking analysis. PMID:32773989
Structural insight to hydroxychloroquine-3C-like proteinase complexation from SARS-CoV-2: inhibitor modelling study through molecular docking and MD-simulation study. PMID:32772895
Insight into the structures of Interleukin-18 systems. PMID:32769049
NCKAP1L defects lead to a novel syndrome combining immunodeficiency, lymphoproliferation, and hyperinflammation. PMID:32766723
Zinc-mediated conformational preselection mechanism in the allosteric control of DNA binding to the zinc transcriptional regulator (ZitR). PMID:32764589
[Comparative analysis of structural characteristics and epitopes in S proteins between SARS-CoV-2 and SARS-CoV]. PMID:32762171
[Quantitative determination and optimun extraction technique of nine compounds of Paeoniae Radix Alba]. PMID:32762162
Integrative illustration for coronavirus outreach. PMID:32760062
Long QT Syndrome Type 2: Emerging Strategies for Correcting Class 2 KCNH2 (hERG) Mutations and Identifying New Patients. PMID:32759882
In silico molecular docking analysis for repurposing therapeutics against multiple proteins from SARS-CoV-2. PMID:32758569
How to measure and evaluate binding affinities. PMID:32758356
Two rare PROX1 variants in patients with lymphedema. PMID:32757260
PremPRI: Predicting the Effects of Missense Mutations on Protein-RNA Interactions. PMID:32756481
ConoMode, a database for conopeptide binding modes. PMID:32754758
Comparative Genomics and Evolutionary Analysis of RNA-Binding Proteins of the CsrA Family in the Genus Pseudomonas. PMID:32754614
Identification of SARS-CoV-2 Cell Entry Inhibitors by Drug Repurposing Using in silico Structure-Based Virtual Screening Approach. PMID:32754161
Insights into the Effect of Curcumin and (-)-Epigallocatechin-3-Gallate on the Aggregation of Aβ(1-40) Monomers by Means of Molecular Dynamics. PMID:32751722
Moonlighting Proteins in the Fuzzy Logic of Cellular Metabolism. PMID:32751110
32A9, a novel human antibody for designing an immunotoxin and CAR-T cells against glypican-3 in hepatocellular carcinoma. PMID:32746924
Orientation of immobilized antigens on common surfaces by a simple computational model: Exposition of SARS-CoV-2 Spike protein RBD epitopes. PMID:32745829
Native Cell Membrane Nanoparticles System for Membrane Protein-Protein Interaction Analysis. PMID:32744521
Validation tests for cryo-EM maps using an independent particle set. PMID:32743544
Network-based protein structural classification. PMID:32742675
Prioritizing potential ACE2 inhibitors in the COVID-19 pandemic: Insights from a molecular mechanics-assisted structure-based virtual screening experiment. PMID:32739642
Benchmarking GPCR homology model template selection in combination with de novo loop generation. PMID:32737667
Gap junctions deliver malonyl-CoA from soma to germline to support embryogenesis in Caenorhabditis elegans. PMID:32735213
The Bio3D packages for structural bioinformatics. PMID:32734663
Opportunities and challenges for assigning cofactors in cryo-EM density maps of chlorophyll-containing proteins. PMID:32733087
The Flavoproteome of the Model Plant Arabidopsis thaliana. PMID:32731628
Evidence Supporting an Antimicrobial Origin of Targeting Peptides to Endosymbiotic Organelles. PMID:32731621
Frequency and hydrogen bonding of nucleobase homopairs in small molecule crystals. PMID:32725210
Contributions of de novo variants to systemic lupus erythematosus. PMID:32724065
The structural basis of the genetic code: amino acid recognition by aminoacyl-tRNA synthetases. PMID:32724042
Virtual Screening of C. Sativa Constituents for the Identification of Selective Ligands for Cannabinoid Receptor 2. PMID:32722631
A Computational Approach to Identify Potential Novel Inhibitors against the Coronavirus SARS-CoV-2. PMID:32721082
Vaccine candidate designed against carcinoembryonic antigen-related cell adhesion molecules using immunoinformatics tools. PMID:32720576
Tumorigenic p53 mutants undergo common structural disruptions including conversion to α-sheet structure. PMID:32715544
Study on the Selection of the Targets of Esophageal Carcinoma and Interventions of Ginsenosides Based on Network Pharmacology and Bioinformatics. PMID:32714406
PertInInt: An Integrative, Analytical Approach to Rapidly Uncover Cancer Driver Genes with Perturbed Interactions and Functionalities. PMID:32711844
Causal mutations from adaptive laboratory evolution are outlined by multiple scales of genome annotations and condition-specificity. PMID:32711472
Side chain flexibility and the symmetry of protein homodimers. PMID:32706779
Mechanistic insights into Lhr helicase function in DNA repair. PMID:32706021
Molecular docking and dynamics study of natural compound for potential inhibition of main protease of SARS-CoV-2. PMID:32705962
Computational drug repurposing for the identification of SARS-CoV-2 main protease inhibitors. PMID:32705942
Data Set Augmentation Allows Deep Learning-Based Virtual Screening to Better Generalize to Unseen Target Classes and Highlight Important Binding Interactions. PMID:32701288
Analysis of Protein Disorder Predictions in the Light of a Protein Structural Alphabet. PMID:32698546
An NMR-based approach reveals the core structure of the functional domain of SINEUP lncRNAs. PMID:32697302
How to Annotate and Submit a Short Linear Motif to the Eukaryotic Linear Motif Resource. PMID:32696353
The PPAR Ω Pocket: Renewed Opportunities for Drug Development. PMID:32695150
Structure-Based Virtual Screening to Discover Potential Lead Molecules for the SARS-CoV-2 Main Protease. PMID:32687345
Guidelines To Predict Binding Poses of Antibody-Integrin Complexes. PMID:32685800
Therapeutic potential of targeting MKK3-p38 axis with Capsaicin for Nasopharyngeal Carcinoma. PMID:32685028
Comparative Assessment of Protein Kinase Inhibitors in Public Databases and in PKIDB. PMID:32679723
Designing a multi-epitope vaccine against SARS-CoV-2: an immunoinformatics approach. PMID:32677533
A Broad Temperature Active Lipase Purified From a Psychrotrophic Bacterium of Sikkim Himalaya With Potential Application in Detergent Formulation. PMID:32671041
Machine learning classification can reduce false positives in structure-based virtual screening. PMID:32669436
High Throughput Virtual Screening to Discover Inhibitors of the Main Protease of the Coronavirus SARS-CoV-2. PMID:32668701
HLA-Arena: A Customizable Environment for the Structural Modeling and Analysis of Peptide-HLA Complexes for Cancer Immunotherapy. PMID:32667823
Selection for Reducing Energy Cost of Protein Production Drives the GC Content and Amino Acid Composition Bias in Gene Transfer Agents. PMID:32665274
The Grapefruit Effect: Interaction between Cytochrome P450 and Coumarin Food Components, Bergamottin, Fraxidin and Osthole. X-ray Crystal Structure and DFT Studies. PMID:32664320
An Irreversible Inhibitor to Probe the Role of Streptococcus pyogenes Cysteine Protease SpeB in Evasion of Host Complement Defenses. PMID:32662975
Computational discovery of small drug-like compounds as potential inhibitors of SARS-CoV-2 main protease. PMID:32662333
A simple open source bioinformatic methodology for initial exploration of GPCR ligands' agonistic/antagonistic properties. PMID:32662237
Discovery of Novel Non-Steroidal Cytochrome P450 17A1 Inhibitors as Potential Prostate Cancer Agents. PMID:32660148
Super Secondary Structures of Proteins with Post-Translational Modifications in Colon Cancer. PMID:32660089
Inactivation of the dimeric RappLS20 anti-repressor of the conjugation operon is mediated by peptide-induced tetramerization. PMID:32658272
Boosting the accuracy of protein secondary structure prediction through nearest neighbor search and method hybridization. PMID:32657384
SARS-CoV and SARS-CoV-2 main protease residue interaction networks change when bound to inhibitor N3. PMID:32653646
Virtual Screening of Human Class-A GPCRs Using Ligand Profiles Built on Multiple Ligand-Receptor Interactions. PMID:32652079
Augmented base pairing networks encode RNA-small molecule binding preferences. PMID:32652015
Mapping of Recognition Sites of Monoclonal Antibodies Responsible for the Inhibition of Pneumolysin Functional Activity. PMID:32650398
On the complementarity of X-ray and NMR data. PMID:32647823
Parsing the functional specificity of Siderocalin/Lipocalin 2/NGAL for siderophores and related small-molecule ligands. PMID:32647813
West-Life: A Virtual Research Environment for structural biology. PMID:32647812
Evolving geographic diversity in SARS-CoV2 and in silico analysis of replicating enzyme 3CLpro targeting repurposed drug candidates. PMID:32646487
Machine learning and AI-based approaches for bioactive ligand discovery and GPCR-ligand recognition. PMID:32645448
Predicting the Substrate Scope of the Flavin-Dependent Halogenase BrvH. PMID:32645255
Leveraging Systematic Functional Analysis to Benchmark an In Silico Framework Distinguishes Driver from Passenger MEK Mutants in Cancer. PMID:32641410
Aldose Reductase Differential Inhibitors in Green Tea. PMID:32640594
Visualisation tools for dependent peptide searches to support the exploration of in vitro protein modifications. PMID:32639981
Milk Processing Affects Structure, Bioavailability and Immunogenicity of β-lactoglobulin. PMID:32635246
Full Rescue of F508del-CFTR Processing and Function by CFTR Modulators Can Be Achieved by Removal of Two Regulatory Regions. PMID:32630527
The Structure of Amyloid Versus the Structure of Globular Proteins. PMID:32630137
Dark Proteome Database: Studies on Disorder. PMID:32629790
Sequence Compression Benchmark (SCB) database-A comprehensive evaluation of reference-free compressors for FASTA-formatted sequences. PMID:32627830
Backbone and sidechain resonance assignments and secondary structure of Scc4 from Chlamydia trachomatis. PMID:32617786
In silico structural modeling and analysis of physicochemical properties of curcumin synthase (CURS1, CURS2, and CURS3) proteins of Curcuma longa. PMID:32617758
Characterizations of SARS-CoV-2 mutational profile, spike protein stability and viral transmission. PMID:32615316
Lignin Biodegradation by a Cytochrome P450 Enzyme: A Computational Study into Syringol Activation by GcoA. PMID:32613677
Proteus: An algorithm for proposing stabilizing mutation pairs based on interactions observed in known protein 3D structures. PMID:32611389
Glutantβase: a database for improving the rational design of glucose-tolerant β-glucosidases. PMID:32611314
Network analysis of synonymous codon usage. PMID:32609328
Neuronal α2δ proteins and brain disorders. PMID:32607809
Evaluating the Potential for Cross-Interactions of Antitoxins in Type II TA Systems. PMID:32604745
Novel phosphatidylinositol 4-kinases III beta (PI4KIIIβ) inhibitors discovered by virtual screening using free energy models. PMID:32601839
In vitro evaluation and molecular docking of QS-21 and quillaic acid from Quillaja saponaria Molina as gastric cancer agents. PMID:32601436
Hub Proteins Involved in RAW 264.7 Macrophages Exposed to Direct Current Electric Field. PMID:32599940
Computational structure modeling for diverse categories of macromolecular interactions. PMID:32599506
Designing a novel mRNA vaccine against SARS-CoV-2: An immunoinformatics approach. PMID:32599237
Structure and Dynamics of a Thermostable Alcohol Dehydrogenase from the Antarctic Psychrophile Moraxella sp. TAE123. PMID:32596590
Bioactivity and Molecular Docking Studies of Derivatives from Cinnamic and Benzoic Acids. PMID:32596343
In vitro targeted screening and molecular docking of stilbene, quinones, and flavonoid on 3T3-L1 pre-adipocytes for anti-adipogenic actions. PMID:32588069
Molecular Determinants Elucidate the Selectivity in Abscisic Acid Receptor and HAB1 Protein Interactions. PMID:32582630
Bioprospecting Microbial Diversity for Lignin Valorization: Dry and Wet Screening Methods. PMID:32582068
Cellular and Molecular Targets of Waterbuck Repellent Blend Odors in Antennae of Glossina fuscipes fuscipes Newstead, 1910. PMID:32581714
Structure-Based Discovery of Dual-Target Hits for Acetylcholinesterase and the α7 Nicotinic Acetylcholine Receptors: In Silico Studies and In Vitro Confirmation. PMID:32580406
Applications of the Pharmacophore Concept in Natural Product inspired Drug Design. PMID:32578959
Impacts of drug resistance mutations on the structural asymmetry of the HIV-2 protease. PMID:32576133
Benchmarking Data Sets from PubChem BioAssay Data: Current Scenario and Room for Improvement. PMID:32575564
Elucidation of cellular targets and exploitation of the receptor-binding domain of SARS-CoV-2 for vaccine and monoclonal antibody synthesis. PMID:32573788
ProbeRating: a recommender system to infer binding profiles for nucleic acid-binding proteins. PMID:32573679
Targeting SARS-COV-2 non-structural protein 16: a virtual drug repurposing study. PMID:32573355
SDCBP/MDA-9/syntenin phosphorylation by AURKA promotes esophageal squamous cell carcinoma progression through the EGFR-PI3K-Akt signaling pathway. PMID:32572158
Constituents of buriti oil (Mauritia flexuosa L.) like inhibitors of the SARS-Coronavirus main peptidase: an investigation by docking and molecular dynamics. PMID:32567501
Computational Drug Repositioning for Chagas Disease Using Protein-Ligand Interaction Profiling. PMID:32560043
Insights from 20 years of the Molecule of the Month. PMID:32558264
HIV-1 Gag mutations alone are sufficient to reduce darunavir susceptibility during virological failure to boosted PI therapy. PMID:32556165
Theoretical insights on helix repacking as the origin of P-glycoprotein promiscuity. PMID:32555203
Constructing artificial respiratory chain in polymer compartments: Insights into the interplay between bo 3 oxidase and the membrane. PMID:32554497
Evaluation of 3-Dimensionality in Approved and Experimental Drug Space. PMID:32551014
Computer-Aided Fragment Growing Strategies to Design Dual Inhibitors of Soluble Epoxide Hydrolase and LTA4 Hydrolase. PMID:32551007
Structural compliance: A new metric for protein flexibility. PMID:32548853
Nicotinamide N-Methyltransferase: Genomic Connection to Disease. PMID:32547055
An in silico approach for identification of novel inhibitors as potential therapeutics targeting COVID-19 main protease. PMID:32544024
β-Strand-mediated interactions of protein domains. PMID:32543729
Conserved buried water molecules enable the β-trefoil architecture. PMID:32542709
Using Accelerated Molecular Dynamics Simulation to elucidate the effects of the T198F mutation on the molecular flexibility of the West Nile virus envelope protein. PMID:32541675
Structural basis for divergent C-H hydroxylation selectivity in two Rieske oxygenases. PMID:32532989
T cell receptor interactions with human leukocyte antigen govern indirect peptide selectivity for the cancer testis antigen MAGE-A4. PMID:32532817
Linking Biochemical and Structural States of SERCA: Achievements, Challenges, and New Opportunities. PMID:32532023
Immunoinformatics and Structural Analysis for Identification of Immunodominant Epitopes in SARS-CoV-2 as Potential Vaccine Targets. PMID:32526960
Structural basis of prostate-specific membrane antigen recognition by the A9g RNA aptamer. PMID:32525981
A New Family of Jumonji C Domain-Containing KDM Inhibitors Inspired by Natural Product Purpurogallin. PMID:32523934
Leishmanicidal Potential of Hardwickiic Acid Isolated From Croton sylvaticus. PMID:32523532
Genomic determinants of pathogenicity in SARS-CoV-2 and other human coronaviruses. PMID:32522874
ELA/APELA precursor cleaved by furin displays tumor suppressor function in renal cell carcinoma through mTORC1 activation. PMID:32516140
Whole genome sequencing identifies an allele responsible for clear vs. turbid plaque morphology in a Mycobacteriophage. PMID:32513117
IRESbase: A Comprehensive Database of Experimentally Validated Internal Ribosome Entry Sites. PMID:32512182
Genomic determinants of pathogenicity in SARS-CoV-2 and other human coronaviruses. PMID:32511301
Multidomain protein structure prediction using information about residues interacting on multimeric protein interfaces. PMID:32509489
VIRdb: a comprehensive database for interactive analysis of genes/proteins involved in the pathogenesis of vitiligo. PMID:32509450
From the Argonauts Mythological Sailors to the Argonautes RNA-Silencing Navigators: Their Emerging Roles in Human-Cell Pathologies. PMID:32503341
Structural and functional evidence of bacterial antiphage protection by Thoeris defense system via NAD+ degradation. PMID:32499527
Deciphering the Mechanisms of Improved Immunogenicity of Hypochlorous Acid-Treated Antigens in Anti-Cancer Dendritic Cell-Based Vaccines. PMID:32498431
Carbamoyl-Phosphate Synthase 1 as a Novel Target of Phomoxanthone A, a Bioactive Fungal Metabolite. PMID:32498414
Hydrophobic Amino Acids as Universal Elements of Protein-Induced DNA Structure Deformation. PMID:32498246
Harnessing Conformational Plasticity to Generate Designer Enzymes. PMID:32496764
LGR4 deficiency results in delayed puberty through impaired Wnt/β-catenin signaling. PMID:32493844
Determining the unbinding events and conserved motions associated with the pyrazinamide release due to resistance mutations of Mycobacterium tuberculosis pyrazinamidase. PMID:32489525
Conformational distributions of isolated myosin motor domains encode their mechanochemical properties. PMID:32479265
Design of Dual Inhibitors of Histone Deacetylase 6 and Heat Shock Protein 90. PMID:32478236
Identification of potential natural inhibitors of SARS-CoV2 main protease by molecular docking and simulation studies. PMID:32476576
Identification of Selective Novel Hits against Plasmodium falciparum Prolyl tRNA Synthetase Active Site and a Predicted Allosteric Site Using in silico Approaches. PMID:32471245
Chimeric Vaccines Designed by Immunoinformatics-Activated Polyfunctional and Memory T Cells That Trigger Protection against Experimental Visceral Leishmaniasis. PMID:32471081
Coronavirus3D: 3D structural visualization of COVID-19 genomic divergence. PMID:32470119
Optical Control of Lysophosphatidic Acid Signaling. PMID:32469525
In Silico Drug Design for Purinergic GPCRs: Overview on Molecular Dynamics Applied to Adenosine and P2Y Receptors. PMID:32466404
Intrinsic Disorder in Tetratricopeptide Repeat Proteins. PMID:32466138
Structure-based drug repositioning explains ibrutinib as VEGFR2 inhibitor. PMID:32459810
Structural Recognition and Binding Pattern Analysis of Human Topoisomerase II Alpha with Steroidal Drugs: In Silico Study to Switchover the Cancer Treatment. PMID:32458643
Parallel Evolution of Tobramycin Resistance across Species and Environments. PMID:32457248
Potential Inhibitors for Novel Coronavirus Protease Identified by Virtual Screening of 606 Million Compounds. PMID:32455534
Discovery of 20 novel ribosomal leader candidates in bacteria and archaea. PMID:32448158
Identification of phytochemical inhibitors against main protease of COVID-19 using molecular modeling approaches. PMID:32448034
Revealing the Common Mechanisms of Scutellarin in Angina Pectoris and Ischemic Stroke Treatment via a Network Pharmacology Approach. PMID:32447519
ProteinFishing: a protein complex generator within the ModelX toolsuite. PMID:32437555
Epitope-Based Vaccine Designing of Nocardia asteroides Targeting the Virulence Factor Mce-Family Protein by Immunoinformatics Approach. PMID:32435172
Evaluation of new antihypertensive drugs designed in silico using Thermolysin as a target. PMID:32435139
The near-symmetry of protein oligomers: NMR-derived structures. PMID:32433550
Loss of heterozygosity of essential genes represents a widespread class of potential cancer vulnerabilities. PMID:32433464
Enhancing the promiscuity of a member of the Caspase protease family by rational design. PMID:32432825
Design, synthesis, molecular modelling and in vitro screening of monoamine oxidase inhibitory activities of novel quinazolyl hydrazine derivatives. PMID:32431898
Non-active site mutants of HIV-1 protease influence resistance and sensitisation towards protease inhibitors. PMID:32430025
In-Silico Proteomic Exploratory Quest: Crafting T-Cell Epitope Vaccine Against Whipple's Disease. PMID:32427224
In vivo and in silico evaluation of antinociceptive activities of seed extract from the Holarrhena antidysenterica plant. PMID:32426548
Structure of the Hydrophobic Core Determines the 3D Protein Structure-Verification by Single Mutation Proteins. PMID:32423068
Graph-Directed Approach for Downselecting Toxins for Experimental Structure Determination. PMID:32422972
Role of radical quenching activity of dihydrocanaric acid in the treatment of cancer-experimental and theoretical. PMID:32420010
Drug repositioning or target repositioning: A structural perspective of drug-target-indication relationship for available repurposed drugs. PMID:32419905
On the interactions of the receptor-binding domain of SARS-CoV-1 and SARS-CoV-2 spike proteins with monoclonal antibodies and the receptor ACE2. PMID:32416259
Effects of Single Mutations on Protein Stability Are Gaussian Distributed. PMID:32416078
A Systematic and Comprehensive Review on Disease-Causing Genes in Amyotrophic Lateral Sclerosis. PMID:32415434
ABC Transporter DerAB of Lactobacillus casei Mediates Resistance against Insect-Derived Defensins. PMID:32414796
The Role of Gene Elongation in the Evolution of Histidine Biosynthetic Genes. PMID:32414216
Electron Paramagnetic Resonance as a Tool for Studying Membrane Proteins. PMID:32414134
Cannabis Constituents and Acetylcholinesterase Interaction: Molecular Docking, In Vitro Studies and Association with CNR1 rs806368 and ACHE rs17228602. PMID:32414087
Genotype-phenotype analysis of LMNA-related diseases predicts phenotype-selective alterations in lamin phosphorylation. PMID:32413188
Marine natural compounds as potents inhibitors against the main protease of SARS-CoV-2-a molecular dynamic study. PMID:32410504
Shape-preserving elastic solid models of macromolecules. PMID:32407309
MISCAST: MIssense variant to protein StruCture Analysis web SuiTe. PMID:32402084
Using machine learning to improve ensemble docking for drug discovery. PMID:32401384
Revenant: a database of resurrected proteins. PMID:32400867
A massively parallel barcoded sequencing pipeline enables generation of the first ORFeome and interactome map for rice. PMID:32398372
Human-likeness of antibody biologics determined by back-translation and comparison with large antibody variable gene repertoires. PMID:32397786
EnzymeMiner: automated mining of soluble enzymes with diverse structures, catalytic properties and stabilities. PMID:32392342
AlloSigMA 2: paving the way to designing allosteric effectors and to exploring allosteric effects of mutations. PMID:32392302
Self-analysis of repeat proteins reveals evolutionarily conserved patterns. PMID:32381046
In-silico identification of the vaccine candidate epitopes against the Lassa virus hemorrhagic fever. PMID:32376973
Repurposing of chloroquine and some clinically approved antiviral drugs as effective therapeutics to prevent cellular entry and replication of coronavirus. PMID:32375574
Transcriptome of the parasitic flatworm Schistosoma mansoni during intra-mammalian development. PMID:32374726
Molecular Mechanism of Selective Binding of NMS-P118 to PARP-1 and PARP-2: A Computational Perspective. PMID:32373627
Design, antihuman immunodeficiency activity and molecular docking studies of synthesized 2-aryl and 2-pyrimidinyl pyrrolidines. PMID:32372249
RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers. PMID:32371455
Synthesis of the Thomsen-Friedenreich-antigen (TF-antigen) and binding of Galectin-3 to TF-antigen presenting neo-glycoproteins. PMID:32367478
Advances in exploring activity cliffs. PMID:32367387
Olfactory marker protein directly buffers cAMP to avoid depolarization-induced silencing of olfactory receptor neurons. PMID:32366818
Quercetin Blocks Ebola Virus Infection by Counteracting the VP24 Interferon-Inhibitory Function. PMID:32366711
Structural and Evolutionary Analysis Indicate That the SARS-CoV-2 Mpro Is a Challenging Target for Small-Molecule Inhibitor Design. PMID:32353978
A single nucleotide variant of human PARP1 determines response to PARP inhibitors. PMID:32352035
Epitope based vaccine prediction for SARS-COV-2 by deploying immuno-informatics approach. PMID:32352026
PredDBP-Stack: Prediction of DNA-Binding Proteins from HMM Profiles using a Stacked Ensemble Method. PMID:32352006
Computational and in vitro Pharmacodynamics Characterization of 1A-116 Rac1 Inhibitor: Relevance of Trp56 in Its Biological Activity. PMID:32351958
Methanolic Bark Extract of Abroma augusta (L.) Induces Apoptosis in EAC Cells through Altered Expression of Apoptosis Regulatory Genes. PMID:32351610
Adaptations of Escherichia coli strains to oxidative stress are reflected in properties of their structural proteomes. PMID:32349661
Small Conformational Changes Underlie Evolution of Resistance to NNRTI in HIV Reverse Transcriptase. PMID:32348721
Structure-Based Design of Highly Potent HIV-1 Protease Inhibitors Containing New Tricyclic Ring P2-Ligands: Design, Synthesis, Biological, and X-ray Structural Studies. PMID:32348139
Structural analysis of pathogenic missense mutations in GABRA2 and identification of a novel de novo variant in the desensitization gate. PMID:32347641
PDBMD2CD: providing predicted protein circular dichroism spectra from multiple molecular dynamics-generated protein structures. PMID:32343309
Successive Statistical and Structure-Based Modeling to Identify Chemically Novel Kinase Inhibitors. PMID:32343143
Computational Investigation on the p53-MDM2 Interaction Using the Potential of Mean Force Study. PMID:32337406
Entropy, Fluctuations, and Disordered Proteins. PMID:32336912
Design of Angiotensin-converting Enzyme 2 (ACE2) Inhibitors by Virtual Lead Optimization and Screening. PMID:32336762
Biological Characterization, Mechanistic Investigation and Structure-Activity Relationships of Chemically Stable TLR2 Antagonists. PMID:32333508
Predicting Protein Functional Motions: an Old Recipe with a New Twist. PMID:32330413
PyRod Enables Rational Homology Model-based Virtual Screening Against MCHR1. PMID:32329245
Alternaria toxins as casein kinase 2 inhibitors and possible consequences for estrogenicity: a hybrid in silico/in vitro study. PMID:32328700
Gibbs Free Energy Calculation of Mutation in PncA and RpsA Associated With Pyrazinamide Resistance. PMID:32328498
Novel Apoptotic Mediators Identified by Conservation of Vertebrate Caspase Targets. PMID:32326640
FDA-Approved Drugs Efavirenz, Tipranavir, and Dasabuvir Inhibit Replication of Multiple Flaviviruses in Vero Cells. PMID:32326119
GlyGen data model and processing workflow. PMID:32324859
Pharmacodynamics of Ceftiofur Selected by Genomic and Proteomic Approaches of Streptococcus parauberis Isolated from the Flounder, Paralichthys olivaceus. PMID:32318593
Novel Target Exploration from Hypothetical Proteins of Klebsiella pneumoniae MGH 78578 Reveals a Protein Involved in Host-Pathogen Interaction. PMID:32318354
Multitarget Approach to Drug Candidates against Alzheimer's Disease Related to AChE, SERT, BACE1 and GSK3β Protein Targets. PMID:32316402
Protein-Protein Interactions Prediction Based on Graph Energy and Protein Sequence Information. PMID:32316294
Binding-Site Match Maker (BSMM): A Computational Method for the Design of Multi-Target Ligands. PMID:32316104
Using an integrative machine learning approach utilising homology modelling to clinically interpret genetic variants: CACNA1F as an exemplar. PMID:32313206
On the evolution of the quality of macromolecular models in the PDB. PMID:32311227
Peptide-like and small-molecule inhibitors against Covid-19. PMID:32306822
HMMPred: Accurate Prediction of DNA-Binding Proteins Based on HMM Profiles and XGBoost Feature Selection. PMID:32300371
ProteinsPlus: interactive analysis of protein-ligand binding interfaces. PMID:32297936
Analyses of the folding sites of irregular β-trefoil fold proteins through sequence-based techniques and Gō-model simulations. PMID:32295515
Reverse vaccinology approach to design a novel multi-epitope vaccine candidate against COVID-19: an in silico study. PMID:32295479
Checking NEKs: Overcoming a Bottleneck in Human Diseases. PMID:32294979
ASFVdb: an integrative resource for genomic and proteomic analyses of African swine fever virus. PMID:32294195
ppiGReMLIN: a graph mining based detection of conserved structural arrangements in protein-protein interfaces. PMID:32293241
DeepBindPoc: a deep learning method to rank ligand binding pockets using molecular vector representation. PMID:32292649
System Approach for Building of Calcium-Binding Sites in Proteins. PMID:32290360
Structural bioinformatics analysis of free cysteines in protein environments. PMID:32288881
The hypertrophic cardiomyopathy mutations R403Q and R663H increase the number of myosin heads available to interact with actin. PMID:32284968
Further Optimization and Validation of the Classical Drude Polarizable Protein Force Field. PMID:32282198
Evaluating DCA-based method performances for RNA contact prediction by a well-curated data set. PMID:32276988
Formononetin inhibits tumor growth by suppression of EGFR-Akt-Mcl-1 axis in non-small cell lung cancer. PMID:32276600
Potent Anticancer Effect of the Natural Steroidal Saponin Gracillin Is Produced by Inhibiting Glycolysis and Oxidative Phosphorylation-Mediated Bioenergetics. PMID:32276500
SAAMBE-3D: Predicting Effect of Mutations on Protein-Protein Interactions. PMID:32272725
Amyloid β chaperone - lipocalin-type prostaglandin D synthase acts as a peroxidase in the presence of heme. PMID:32271881
The HDOCK server for integrated protein-protein docking. PMID:32269383
Targeting SARS-CoV-2: a systematic drug repurposing approach to identify promising inhibitors against 3C-like proteinase and 2'-O-ribose methyltransferase. PMID:32266873
Multimodular fused acetyl-feruloyl esterases from soil and gut Bacteroidetes improve xylanase depolymerization of recalcitrant biomass. PMID:32266006
Two-Level Protein Methylation Prediction using structure model-based features. PMID:32265459
Chemistry, Biological Activities and In Silico Bioprospection of Sterols and Triterpenes from Mexican Columnar Cactaceae. PMID:32260146
Molecular Topology of RNA Polymerase I Upstream Activation Factor. PMID:32253346
Backbone Free Energy Estimator Applied to Viral Glycoproteins. PMID:32250657
A knowledge-based scoring function to assess quaternary associations of proteins. PMID:32246820
TGPred: a tumor gene prediction webserver for analyzing structural and functional impacts of variants. PMID:32246141
Re-annotation of the Theileria parva genome refines 53% of the proteome and uncovers essential components of N-glycosylation, a conserved pathway in many organisms. PMID:32245418
Combining Virtual Screening Protocol and In Vitro Evaluation towards the Discovery of BACE1 Inhibitors. PMID:32244832
How RNA-Binding Proteins Interact with RNA: Molecules and Mechanisms. PMID:32243832
Phenotypic Screening of Chemical Libraries Enriched by Molecular Docking to Multiple Targets Selected from Glioblastoma Genomic Data. PMID:32243127
The landscape of alternative splicing in HIV-1 infected CD4 T-cells. PMID:32241262
A Humanized Monoclonal Antibody Cocktail to Prevent Pulmonary Ricin Intoxication. PMID:32235318
Ellagic Acid, Kaempferol, and Quercetin from Acacia nilotica: Promising Combined Drug With Multiple Mechanisms of Action. PMID:32226726
Biophysical Techniques for Target Validation and Drug Discovery in Transcription-Targeted Therapy. PMID:32225120
Simple Selection Procedure to Distinguish between Static and Flexible Loops. PMID:32225102
Ionizing Radiation and Complex DNA Damage: Quantifying the Radiobiological Damage Using Monte Carlo Simulations. PMID:32225023
Discovery of potential targets of Triptolide through inverse docking in ovarian cancer cells. PMID:32219016
Prediction of polyproline II secondary structure propensity in proteins. PMID:32218953
Modeling the structure of SARS 3a transmembrane protein using a minimum unfavorable contact approach. PMID:32218650
Inhibition of the activity of HIV-1 protease through antibody binding and mutations probed by molecular dynamics simulations. PMID:32218488
Artificial Intelligence and Machine learning based prediction of resistant and susceptible mutations in Mycobacterium tuberculosis. PMID:32218465
Spatial Expression Pattern of the Major Ca2+-Buffer Proteins in Mouse Retinal Ganglion Cells. PMID:32218175
Cylindrical Similarity Measurement for Helices in Medium-Resolution Cryo-Electron Microscopy Density Maps. PMID:32216344
Accurate Representation of Protein-Ligand Structural Diversity in the Protein Data Bank (PDB). PMID:32213914
Cellular processes involved in lung cancer cells exposed to direct current electric field. PMID:32210363
An Appetite for Destruction: Detecting Prey-Selective Binding of α-Neurotoxins in the Venom of Afro-Asian Elapids. PMID:32210072
Ethnogeographic and inter-individual variability of human ABC transporters. PMID:32206879
Developing and applying computational resources for biochemistry education. PMID:32203640
Quantitative phosphoproteomic analysis identifies the potential therapeutic target EphA2 for overcoming sorafenib resistance in hepatocellular carcinoma cells. PMID:32203105
graphDelta: MPNN Scoring Function for the Affinity Prediction of Protein-Ligand Complexes. PMID:32201802
Aggregation and Cellular Toxicity of Pathogenic or Non-pathogenic Proteins. PMID:32198463
MAINMASTseg: Automated Map Segmentation Method for Cryo-EM Density Maps with Symmetry. PMID:32197044
Breaking the vicious loop between inflammation, oxidative stress and coagulation, a novel anti-thrombus insight of nattokinase by inhibiting LPS-induced inflammation and oxidative stress. PMID:32193146
Discrete analysis of camelid variable domains: sequences, structures, and in-silico structure prediction. PMID:32185102
Uncovering dark multichromophoric states in Peridinin-Chlorophyll-Protein. PMID:32183641
Docking and Molecular Dynamics Predictions of Pesticide Binding to the Calyx of Bovine β-Lactoglobulin. PMID:32183317
Differential Abilities of Mammalian Cathelicidins to Inhibit Bacterial Biofilm Formation and Promote Multifaceted Immune Functions of Neutrophils. PMID:32182913
Delineating elastic properties of kinesin linker and their sensitivity to point mutations. PMID:32179821
PETRA: Drug Engineering via Rigidity Analysis. PMID:32178472
Leucine-rich repeat receptor-like kinase II phylogenetics reveals five main clades throughout the plant kingdom. PMID:32175641
Molecular Modeling Study of Uncharged Oximes Compared to HI-6 and 2-PAM Inside Human AChE Sarin and VX Conjugates. PMID:32175496
Recent Advances in Understanding Biological GTP Hydrolysis through Molecular Simulation. PMID:32175485
Exploring the RNA-Recognition Mechanism Using Supervised Molecular Dynamics (SuMD) Simulations: Toward a Rational Design for Ribonucleic-Targeting Molecules? PMID:32175307
The Atypical Protein Kinase C Small Molecule Inhibitor ζ-Stat, and Its Effects on Invasion Through Decreases in PKC-ζ Protein Expression. PMID:32175276
COMER2: GPU-accelerated sensitive and specific homology searches. PMID:32167522
Mutation effect estimation on protein-protein interactions using deep contextualized representation learning. PMID:32166223
visGReMLIN: graph mining-based detection and visualization of conserved motifs at 3D protein-ligand interface at the atomic level. PMID:32164574
GSP4PDB: a web tool to visualize, search and explore protein-ligand structural patterns. PMID:32164553
Difference contact maps: From what to why in the analysis of the conformational flexibility of proteins. PMID:32163442
Rapid Identification of Potential Inhibitors of SARS-CoV-2 Main Protease by Deep Docking of 1.3 Billion Compounds. PMID:32162456
Phosphoglycerate Mutase 1: Its Glycolytic and Non-Glycolytic Roles in Tumor Malignant Behaviors and Potential Therapeutic Significance. PMID:32161473
Low mutational load and high mutation rate variation in gut commensal bacteria. PMID:32155146
Designs of Antigen Structure and Composition for Improved Protein-Based Vaccine Efficacy. PMID:32153587
Principles of fluoride toxicity and the cellular response: a review. PMID:32152649
NBCZone: Universal three-dimensional construction of eleven amino acids near the catalytic nucleophile and base in the superfamily of (chymo)trypsin-like serine fold proteases. PMID:32151723
1,2,4-Triazolo[1,5-a]pyrimidines as a Novel Class of Inhibitors of the HIV-1 Reverse Transcriptase-Associated Ribonuclease H Activity. PMID:32151066
Functional exploration of the GH29 fucosidase family. PMID:32149359
Computer simulations of protein-membrane systems. PMID:32145948
A Network-Based Approach to Explore the Mechanisms of Uncaria Alkaloids in Treating Hypertension and Alleviating Alzheimer's Disease. PMID:32143538
ClusPro in rounds 38 to 45 of CAPRI: Toward combining template-based methods with free docking. PMID:32142178
Electrostatic Interactions Govern Extreme Nascent Protein Ejection Times from Ribosomes and Can Delay Ribosome Recycling. PMID:32138505
Basic Limonoid modulates Chaperone-mediated Proteostasis and dissolve Tau fibrils. PMID:32132570
A potential role for integrins in host cell entry by SARS-CoV-2. PMID:32130973
Structural Biology in the Multi-Omics Era. PMID:32129623
PHARMIP: An insilico method to predict genetics that underpin adverse drug reactions. PMID:32123669
Applications of water molecules for analysis of macromolecule properties. PMID:32123557
Recent advances in functional research in Giardia intestinalis. PMID:32122532
Structure-based discovery of potent and selective melatonin receptor agonists. PMID:32118583
Exploration of the Molecular Mechanism of FUZI (Aconiti Lateralis Radix Praeparata) in Allergic Rhinitis Treatment Based on Network Pharmacology. PMID:32114589
RFPR-IDP: reduce the false positive rates for intrinsically disordered protein and region prediction by incorporating both fully ordered proteins and disordered proteins. PMID:32112084
Proteome Instability Is a Therapeutic Vulnerability in Mismatch Repair-Deficient Cancer. PMID:32109374
Human papillomavirus E6: Host cell receptor, GRP78, binding site prediction. PMID:32108357
Protective Effect of Genistein against Compound 48/80 Induced Anaphylactoid Shock via Inhibiting MAS Related G Protein-Coupled Receptor X2 (MRGPRX2). PMID:32106575
Charting Hydrogen Bond Anisotropy. PMID:32105473
Structure of the G protein chaperone and guanine nucleotide exchange factor Ric-8A bound to Gαi1. PMID:32103024
TCRs with Distinct Specificity Profiles Use Different Binding Modes to Engage an Identical Peptide-HLA Complex. PMID:32102902
The Central Role of Non-Structural Protein 1 (NS1) in Influenza Biology and Infection. PMID:32098424
Analysis of protein missense alterations by combining sequence- and structure-based methods. PMID:32096919
Evolutionary Relationships Between Low Potential Ferredoxin and Flavodoxin Electron Carriers. PMID:32095484
Large-Scale Virtual Screening Against the MET Kinase Domain Identifies a New Putative Inhibitor Type. PMID:32093126
Molecular Rescue of Dyrk1A Overexpression Alterations in Mice with Fontup® Dietary Supplement: Role of Green Tea Catechins. PMID:32092951
The acid-base-nucleophile catalytic triad in ABH-fold enzymes is coordinated by a set of structural elements. PMID:32084230
Deguelin suppresses non-small cell lung cancer by inhibiting EGFR signaling and promoting GSK3β/FBW7-mediated Mcl-1 destabilization. PMID:32081857
Short and simple sequences favored the emergence of N-helix phospho-ligand binding sites in the first enzymes. PMID:32079722
A computational approach yields selective inhibitors of human excitatory amino acid transporter 2 (EAAT2). PMID:32079674
Dimer Interface Organization is a Main Determinant of Intermonomeric Interactions and Correlates with Evolutionary Relationships of Retroviral and Retroviral-Like Ddi1 and Ddi2 Proteases. PMID:32079302
Evaluating the significance of contact maps in low-homology protein modeling using contact-assisted threading. PMID:32076047
Metagenome Mining Reveals Hidden Genomic Diversity of Pelagimyophages in Aquatic Environments. PMID:32071164
RPI-SE: a stacking ensemble learning framework for ncRNA-protein interactions prediction using sequence information. PMID:32070279
Mucopolysaccharidosis Type II: One Hundred Years of Research, Diagnosis, and Treatment. PMID:32070051
Impact of the Protein Data Bank on antineoplastic approvals. PMID:32068073
Analyses on clustering of the conserved residues at protein-RNA interfaces and its application in binding site identification. PMID:32066366
Reconstructing the evolutionary history of nitrogenases: Evidence for ancestral molybdenum-cofactor utilization. PMID:32065506
Computational Analysis of Crystallization Additives for the Identification of New Allosteric Sites. PMID:32064372
New variants in Spanish Niemann-Pick type c disease patients. PMID:32060698
Inference of Multisite Phosphorylation Rate Constants and Their Modulation by Pathogenic Mutations. PMID:32059766
Metronidazole and Secnidazole Carbamates: Synthesis, Antiprotozoal Activity, and Molecular Dynamics Studies. PMID:32059495
Exploration of databases and methods supporting drug repurposing: a comprehensive survey. PMID:32055842
Electron density learning of non-covalent systems. PMID:32055318
Context-Dependent Gene Regulation by Homeodomain Transcription Factor Complexes Revealed by Shape-Readout Deficient Proteins. PMID:32053778
Long-range correlation in protein dynamics: Confirmation by structural data and normal mode analysis. PMID:32053592
Expanding Role of Ubiquitin in Translational Control. PMID:32050486
Genome-wide inference of the Camponotus floridanus protein-protein interaction network using homologous mapping and interacting domain profile pairs. PMID:32047225
The Remarkable Dual-Level Diversity of Prokaryotic Flagellins. PMID:32047063
Characterizing lineage-specific evolution and the processes driving genomic diversification in chordates. PMID:32046633
Three-Dimensional Krawtchouk Descriptors for Protein Local Surface Shape Comparison. PMID:32042209
Boron nitride nanotubes as containers for targeted drug delivery of doxorubicin. PMID:32036483
The Order-Disorder Continuum: Linking Predictions of Protein Structure and Disorder through Molecular Simulation. PMID:32034199
Weighted persistent homology for biomolecular data analysis. PMID:32034168
In Silico Strategies in Tuberculosis Drug Discovery. PMID:32033144
Probing remote residues important for catalysis in Escherichia coli ornithine transcarbamoylase. PMID:32027716
Identification of tunnels as in potato hydrolases. PMID:32025157
Engineering Biology to Construct Microbial Chassis for the Production of Difficult-to-Express Proteins. PMID:32024292
Protein stability governed by its structural plasticity is inferred by physicochemical factors and salt bridges. PMID:32020026
Alternative Structures of α-Synuclein. PMID:32019169
Elucidating Binding Sites and Affinities of ERα Agonists and Antagonists to Human Alpha-Fetoprotein by In Silico Modeling and Point Mutagenesis. PMID:32019136
Variable impact of conformationally distinct DNA lesions on nucleosome structure and dynamics: Implications for nucleotide excision repair. PMID:32018112
Integrated Computational Approaches and Tools forAllosteric Drug Discovery. PMID:32013012
Antibacterial Peptide Nucleic Acids-Facts and Perspectives. PMID:32012929
The Toxicological Intersection between Allergen and Toxin: A Structural Comparison of the Cat Dander Allergenic Protein Fel d1 and the Slow Loris Brachial Gland Secretion Protein. PMID:32012831
Multiple protein-DNA interfaces unravelled by evolutionary information, physico-chemical and geometrical properties. PMID:32012150
BioMagResBank (BMRB) as a Resource for Structural Biology. PMID:32006287
Dual protease type XIII/pepsin digestion offers superior resolution and overlap for the analysis of histone tails by HX-MS. PMID:32004545
Halogen Bonds in Ligand-Protein Systems: Molecular Orbital Theory for Drug Design. PMID:32003997
PIM1, CYP1B1, and HSPA2 Targeted by Quercetin Play Important Roles in Osteoarthritis Treatment by Achyranthes bidentata. PMID:31998395
Prediction of the secondary structure of short DNA aptamers. PMID:31984183
Normal mode analysis calculation for a full-atom model with a smaller number of degrees of freedom for huge protein molecules. PMID:31984173
Innovative Three-Step Microwave-Promoted Synthesis of N-Propargyltetrahydroquinoline and 1,2,3-Triazole Derivatives as a Potential Factor Xa (FXa) Inhibitors: Drug Design, Synthesis, and Biological Evaluation. PMID:31979319
The hidden world of membrane microproteins. PMID:31978386
Sodium-induced population shift drives activation of thrombin. PMID:31974511
Assessing Structural Determinants of Zn2+ Binding to Human HV1 via Multiple MD Simulations. PMID:31972155
The oxygen-oxygen distance of water in crystallographic data sets. PMID:31970272
A possible role for autoimmunity through molecular mimicry in alphavirus mediated arthritis. PMID:31969581
A Structural Study on the Listeria Monocytogenes Internalin A-Human E-cadherin Interaction: A Molecular Tool to Investigate the Effects of Missense Mutations. PMID:31968631
p-Methoxycinnamic Acid Diesters Lower Dyslipidemia, Liver Oxidative Stress and Toxicity in High-Fat Diet Fed Mice and Human Peripheral Blood Lymphocytes. PMID:31968556
Is the E. coli Homolog of the Formate/Nitrite Transporter Family an Anion Channel? A Computational Study. PMID:31968229
Conformational analysis of macrocycles: comparing general and specialized methods. PMID:31965404
Atomic-level reconstruction of biomolecules by a rigid-fragment- and local-frame-based (RF-LF) strategy. PMID:31965325
NMR Observation of Intermolecular Hydrogen Bonds between Protein Tyrosine Side-Chain OH and DNA Phosphate Groups. PMID:31958014
Computational Analysis of the Silver Nanoparticle-Human Serum Albumin Complex. PMID:31956763
Asymmetric ligand binding in homodimeric Enterobacter cloacae nitroreductase yields the Michaelis complex for nitroaromatic substrates. PMID:31953608
Variation among S-locus haplotypes and among stylar RNases in almond. PMID:31953457
RNA CoSSMos 2.0: an improved searchable database of secondary structure motifs in RNA three-dimensional structures. PMID:31950189
Coumarins from Magydaris pastinacea as inhibitors of the tumour-associated carbonic anhydrases IX and XII: isolation, biological studies and in silico evaluation. PMID:31948300
Elucidating the Structural Basis of the Intracellular pH Sensing Mechanism of TASK-2 K2P Channels. PMID:31947679
Improved protein structure prediction using potentials from deep learning. PMID:31942072
PMFF: Development of a Physics-Based Molecular Force Field for Protein Simulation and Ligand Docking. PMID:31939671
Uncovering the Pharmacological Mechanism of Stemazole in the Treatment of Neurodegenerative Diseases Based on a Network Pharmacology Approach. PMID:31936558
Neuroprotective γ-Pyrones from Fusarium Solani JS-0169: Cell-Based Identification of Active Compounds and an Informatics Approach to Predict the Mechanism of Action. PMID:31935895
Best practices for high data-rate macromolecular crystallography (HDRMX). PMID:31934601
Beyond the heterodimer model for mineralocorticoid and glucocorticoid receptor interactions in nuclei and at DNA. PMID:31923266
Structural Dynamics Behind Clinical Mutants of PncA-Asp12Ala, Pro54Leu, and His57Pro of Mycobacterium tuberculosis Associated With Pyrazinamide Resistance. PMID:31921809
Clinical Assessments and EEG Analyses of Encephalopathies Associated With Dynamin-1 Mutation. PMID:31920647
Structural Aspects of Plant Hormone Signal Perception and Regulation by Ubiquitin Ligases. PMID:31919187
Preclinical development of a humanized chimeric antigen receptor against B cell maturation antigen for multiple myeloma. PMID:31919085
Deep neural network affinity model for BACE inhibitors in D3R Grand Challenge 4. PMID:31916049
The Role of Electrostatics and Folding Kinetics on the Thermostability of Homologous Cold Shock Proteins. PMID:31910002
Web-ARM: A Web-Based Interface for the Automatic Construction of QM/MM Models of Rhodopsins. PMID:31909998
Molecular modelling and docking analysis of pleurocidin (an antimicrobial peptide) like peptides with enterotoxin H from Klebsilla pneumonia. PMID:31902985
Androgen Receptor Dependence. PMID:31900916
Conserved genomic neighborhood is a strong but no perfect indicator for a direct interaction of microbial gene products. PMID:31900122
Improved protein structure prediction using predicted interresidue orientations. PMID:31896580
Structural characterization of glycinamide-RNase-transformylase T from Mycobacterium tuberculosis. PMID:31894729
Combined Linear Interaction Energy and Alchemical Solvation Free-Energy Approach for Protein-Binding Affinity Computation. PMID:31894691
Identification of watermelon heat shock protein members and tissue-specific gene expression analysis under combined drought and heat stresses. PMID:31892809
Modeling beta-sheet peptide-protein interactions: Rosetta FlexPepDock in CAPRI rounds 38-45. PMID:31891416
Volumetric Segmentation via Neural Networks Improves Neutron Crystallography Data Analysis. PMID:31886471
Zika Virus Targeting by Screening Inhibitors against NS2B/NS3 Protease. PMID:31886207
Study on the Multitarget Mechanism and Key Active Ingredients of Herba Siegesbeckiae and Volatile Oil against Rheumatoid Arthritis Based on Network Pharmacology. PMID:31885670
Crystal structure of the N-terminal domain of the trypanosome flagellar protein BILBO1 reveals a ubiquitin fold with a long structured loop for protein binding. PMID:31882537
Cell-permeable high-affinity tracers for Gq proteins provide structural insights, reveal distinct binding kinetics and identify small molecule inhibitors. PMID:31881095
Promising New Inhibitors of Tyrosyl-DNA Phosphodiesterase I (Tdp 1) Combining 4-Arylcoumarin and Monoterpenoid Moieties as Components of Complex Antitumor Therapy. PMID:31878088
Biochemical and Structural Characterization of OXA-405, an OXA-48 Variant with Extended-Spectrum β-Lactamase Activity. PMID:31877796
Pushing the accuracy limit of shape complementarity for protein-protein docking. PMID:31874620
Exploring electrostatic patterns of human, murine, equine and canine TLR4/MD-2 receptors. PMID:31874581
Structural basis of methotrexate and pemetrexed action on serine hydroxymethyltransferases revealed using plant models. PMID:31873125
Lessons from equilibrium statistical physics regarding the assembly of protein complexes. PMID:31871201
Shared unfolding pathways of unrelated immunoglobulin-like β-sandwich proteins. PMID:31868211
Fumagillin, a Mycotoxin of Aspergillus fumigatus: Biosynthesis, Biological Activities, Detection, and Applications. PMID:31861936
Systems-level analysis of NalD mutation, a recurrent driver of rapid drug resistance in acute Pseudomonas aeruginosa infection. PMID:31860667
Dual action of amitriptyline on NMDA receptors: enhancement of Ca-dependent desensitization and trapping channel block. PMID:31857688
Small molecules that inhibit TNF signalling by stabilising an asymmetric form of the trimer. PMID:31857588
Bigram-PGK: phosphoglycerylation prediction using the technique of bigram probabilities of position specific scoring matrix. PMID:31856704
An Activity-Based Sensing Approach for the Detection of Cyclooxygenase-2 in Live Cells. PMID:31854058
Modeling aspects of the language of life through transfer-learning protein sequences. PMID:31847804
Synthesis, X-ray crystal structure, Hirshfeld surface analysis, and molecular docking study of novel inhibitor of hepatitis B: methyl 4-fluoro-3-(morpholinosulfonyl)benzo[b]thiophene-2-carboxylate. PMID:31844693
Model of Early Stage Intermediate in Respect to Its Final Structure. PMID:31842350
Electrostatic Surface Potential of Macrophages Correlates with Their Functional Phenotype. PMID:31838662
A platform for target prediction of phenotypic screening hit molecules. PMID:31836397
Evaluation of serial crystallographic structure determination within megahertz pulse trains. PMID:31832488
Combined e-pharmacophore based screening and docking of PI3 kinase with potential inhibitors from a database of natural compounds. PMID:31831952
Dynamics, nanomechanics and signal transduction in reelin repeats. PMID:31831824
Predicting and designing therapeutics against the Nipah virus. PMID:31830030
Theoretical Study of the Antioxidant Activity of Quercetin Oxidation Products. PMID:31828060
Comparison Study of Computational Prediction Tools for Drug-Target Binding Affinities. PMID:31824921
Analysis of Secondary Structure Biases in Naturally Presented HLA-I Ligands. PMID:31824508
Multifaceted antibodies development against synthetic α-dystroglycan mucin glycopeptide as promising tools for dystroglycanopathies diagnostic. PMID:31823246
Dynamical comparison between Drosha and Dicer reveals functional motion similarities and dissimilarities. PMID:31821368
Sequence specificity in DNA-drug intercalation: MD simulation and density functional theory approaches. PMID:31820194
A History of Molecular Chaperone Structures in the Protein Data Bank. PMID:31817979
Life in Phases: Intra- and Inter- Molecular Phase Transitions in Protein Solutions. PMID:31817975
Newly Developed CK1-Specific Inhibitors Show Specifically Stronger Effects on CK1 Mutants and Colon Cancer Cell Lines. PMID:31817920
Discovery of 8-Amino-Substituted 2-Phenyl-2,7-Naphthyridinone Derivatives as New c-Kit/VEGFR-2 Kinase Inhibitors. PMID:31817456
In Vitro Antidiabetic, Anti-Obesity and Antioxidant Analysis of Ocimum basilicum Aerial Biomass and in Silico Molecular Docking Simulations with Alpha-Amylase and Lipase Enzymes. PMID:31817095
Antibody Structure and Function: The Basis for Engineering Therapeutics. PMID:31816964
The Amyloid as a Ribbon-Like Micelle in Contrast to Spherical Micelles Represented by Globular Proteins. PMID:31816829
Structure-Based Design, Synthesis, and Biological Evaluation of Triazole-Based smHDAC8 Inhibitors. PMID:31816172
Structural insights and binding analysis for determining the molecular bases for programmed cell death protein ligand-1 inhibition. PMID:31814954
Experimental Evidence of Solvent-Separated Ion Pairs as Metastable States in Electrostatic Interactions of Biological Macromolecules. PMID:31809050
Determining the pathogenicity of CFTR missense variants: Multiple comparisons of in silico predictors and variant annotation databases. PMID:31808782
TRIC-A Channel Maintains Store Calcium Handling by Interacting With Type 2 Ryanodine Receptor in Cardiac Muscle. PMID:31805819
Design, Synthesis, and In Vitro Activity of Pyrazine Compounds. PMID:31805633
Sequence-Derived Markers of Drug Targets and Potentially Druggable Human Proteins. PMID:31803227
Modeling the Architecture of Depolymerase-Containing Receptor Binding Proteins in Klebsiella Phages. PMID:31803168
RAACBook: a web server of reduced amino acid alphabet for sequence-dependent inference by using Chou's five-step rule. PMID:31802128
Conformation-dependent restraints for polynucleotides: the sugar moiety. PMID:31799624
Rare GBA1 genotype associated with severe bone disease in Gaucher disease type 1. PMID:31799121
Multi-dimensional computational pipeline for large-scale deep screening of compound effect assessment: an in silico case study on ageing-related compounds. PMID:31798962
Discovery and Characterisation of Dual Inhibitors of Tryptophan 2,3-Dioxygenase (TDO2) and Indoleamine 2,3-Dioxygenase 1 (IDO1) Using Virtual Screening. PMID:31795096
A Dynamic Switch in Inactive p38γ Leads to an Excited State on the Pathway to an Active Kinase. PMID:31794659
PepPro: A Nonredundant Structure Data Set for Benchmarking Peptide-Protein Computational Docking. PMID:31793016
Inhibitor discovery for the E. coli meningitis virulence factor IbeA from homology modeling and virtual screening. PMID:31792885
A common root for coevolution and substitution rate variability in protein sequence evolution. PMID:31792239
Analysing non-synonymous mutations in XDR and MDR tuberculosis drugs. PMID:31788566
Conjugable A3 adenosine receptor antagonists for the development of functionalized ligands and their use in fluorescent probes. PMID:31787357
Characterizing and Predicting Protein Hinges for Mechanistic Insight. PMID:31786268
D3R Grand Challenge 4: ligand similarity and MM-GBSA-based pose prediction and affinity ranking for BACE-1 inhibitors. PMID:31781990
pH-depended protein shell dis- and reassembly of ferritin nanoparticles revealed by atomic force microscopy. PMID:31780685
Trypanocidal Mechanism of Action and in silico Studies of p-Coumaric Acid Derivatives. PMID:31775321
Chemoenzymatic Semisynthesis of Proteins. PMID:31774265
An omics perspective on drug target discovery platforms. PMID:31774113
SXGBsite: Prediction of Protein-Ligand Binding Sites Using Sequence Information and Extreme Gradient Boosting. PMID:31771119
Formation of Prenylated Chalcone Xanthohumol Cocrystals: Single Crystal X-Ray Diffraction, Vibrational Spectroscopic Study Coupled with Multivariate Analysis. PMID:31766540
Cellular Processes Involved in Jurkat Cells Exposed to Nanosecond Pulsed Electric Field. PMID:31766457
Hits Discovery on the Androgen Receptor: In Silico Approaches to Identify Agonist Compounds. PMID:31766271
[b]-Annulated Halogen-Substituted Indoles as Potential DYRK1A Inhibitors. PMID:31766108
Molecular docking study of lamellarin analogues and identification of potential inhibitors of HIV-1 integrase strand transfer complex by virtual screening. PMID:31763475
A3 adenosine receptor activation mechanisms: molecular dynamics analysis of inactive, active, and fully active states. PMID:31758354
Virtual Screening Using Pharmacophore Models Retrieved from Molecular Dynamic Simulations. PMID:31757043
Maximum Entropy Optimized Force Field for Intrinsically Disordered Proteins. PMID:31756104
Carnosic Acid Attenuates Cadmium Induced Nephrotoxicity by Inhibiting Oxidative Stress, Promoting Nrf2/HO-1 Signalling and Impairing TGF-β1/Smad/Collagen IV Signalling. PMID:31752142
Large-Scale Conformational Changes and Protein Function: Breaking the in silico Barrier. PMID:31750315
A Review on Viral Metagenomics in Extreme Environments. PMID:31749771
Protein docking model evaluation by 3D deep convolutional neural networks. PMID:31746961
Identification of lipid A deacylase as a novel, highly conserved and protective antigen against enterohemorrhagic Escherichia coli. PMID:31745113
Self-identity barcodes encoded by six expansive polymorphic toxin families discriminate kin in myxobacteria. PMID:31744876
Novel sampling strategies and a coarse-grained score function for docking homomers, flexible heteromers, and oligosaccharides using Rosetta in CAPRI rounds 37-45. PMID:31742764
Insight into the dimer dissociation process of the Chromobacterium violaceum (S)-selective amine transaminase. PMID:31740704
ADAPTABLE: a comprehensive web platform of antimicrobial peptides tailored to the user's research. PMID:31740563
A New Look at the Structures of Old Sepsis Actors by Exploratory Data Analysis Tools. PMID:31739644
Antimicrobial Peptides as Anti-Infective Agents in Pre-Post-Antibiotic Era? PMID:31739573
Fast Screening of Inhibitor Binding/Unbinding Using Novel Software Tool CaverDock. PMID:31737596
Novel Compound Heterozygous Mutations in IL-7 Receptor α Gene in a 15-Month-Old Girl Presenting With Thrombocytopenia, Normal T Cell Count and Maternal Engraftment. PMID:31736942
HIV-1 Nef Targets HDAC6 to Assure Viral Production and Virus Infection. PMID:31736889
Semi-rational design and molecular dynamics simulations study of the thermostability enhancement of cellobiose 2-epimerases. PMID:31733243
Protein-assisted RNA fragment docking (RnaX) for modeling RNA-protein interactions using ModelX. PMID:31732673
Protein Stability in Titan's Subsurface Water Ocean. PMID:31730377
Nonparametric chemical descriptors for the calculation of ligand-biopolymer affinities with machine-learning scoring functions. PMID:31728812
Cross-docking benchmark for automated pose and ranking prediction of ligand binding. PMID:31721338
Coupling enhanced sampling of the apo-receptor with template-based ligand conformers selection: performance in pose prediction in the D3R Grand Challenge 4. PMID:31720895
A comprehensive analysis of amino-peptidase N1 protein (APN) from Anopheles culicifacies for epitope design using Immuno-informatics models. PMID:31719771
Discovery of Novel µ-Opioid Receptor Inverse Agonist from a Combinatorial Library of Tetrapeptides through Structure-Based Virtual Screening. PMID:31717871
C60 Fullerene as an Effective Nanoplatform of Alkaloid Berberine Delivery into Leukemic Cells. PMID:31717305
Drug Discovery and Repurposing Inhibits a Major Gut Pathogen-Derived Oncogenic Toxin. PMID:31709196
Further Elucidation of the Argonaute and Dicer Protein Families in the Model Grass Species Brachypodium distachyon. PMID:31708948
Intranasal Peptide-Based FpvA-KLH Conjugate Vaccine Protects Mice From Pseudomonas aeruginosa Acute Murine Pneumonia. PMID:31708925
Substrate structure-activity relationship reveals a limited lipopolysaccharide chemotype range for intestinal alkaline phosphatase. PMID:31704704
Carotenoids as Novel Therapeutic Molecules Against Neurodegenerative Disorders: Chemistry and Molecular Docking Analysis. PMID:31703296
ConSurf-DB: An accessible repository for the evolutionary conservation patterns of the majority of PDB proteins. PMID:31702846
Correlation of MLH1 polymorphisms, survival statistics, in silico assessment and gene downregulation with clinical outcomes among breast cancer cases. PMID:31701475
iPBAvizu: a PyMOL plugin for an efficient 3D protein structure superimposition approach. PMID:31700529
Nanoparticle transport phenomena in confined flows. PMID:31692964
D3R Grand Challenge 4: prospective pose prediction of BACE1 ligands with AutoDock-GPU. PMID:31691920
The IUPHAR/BPS Guide to PHARMACOLOGY in 2020: extending immunopharmacology content and introducing the IUPHAR/MMV Guide to MALARIA PHARMACOLOGY. PMID:31691834
Structural characterization of the RH1-LZI tandem of JIP3/4 highlights RH1 domains as a cytoskeletal motor-binding motif. PMID:31690808
Understanding the Effect of Structural Diversity in WRKY Transcription Factors on DNA Binding Efficiency through Molecular Dynamics Simulation. PMID:31690005
Variation in the LRR region of Pi54 protein alters its interaction with the AvrPi54 protein revealed by in silico analysis. PMID:31689303
Extracellular binding of indinavir to matrix metalloproteinase-2 and the alpha-7-nicotinic acetylcholine receptor: implications for use in cancer treatment. PMID:31687607
N-GlyDE: a two-stage N-linked glycosylation site prediction incorporating gapped dipeptides and pattern-based encoding. PMID:31685900
Biochemical characterisation of four rhamnosidases from thermophilic bacteria of the genera Thermotoga, Caldicellulosiruptor and Thermoclostridium. PMID:31685873
Gene Expression Signature-Based Approach Identifies Antifungal Drug Ciclopirox As a Novel Inhibitor of HMGA2 in Colorectal Cancer. PMID:31684108
Crystal Structure Of Photorespiratory Alanine:Glyoxylate Aminotransferase 1 (AGT1) From Arabidopsis thaliana. PMID:31681359
Comparative Analysis of the CDR Loops of Antigen Receptors. PMID:31681328
MaveDB: an open-source platform to distribute and interpret data from multiplexed assays of variant effect. PMID:31679514
Structure and activity of PPX/GppA homologs from Escherichia coli and Helicobacter pylori. PMID:31679177
Performance evaluation of molecular docking and free energy calculations protocols using the D3R Grand Challenge 4 dataset. PMID:31677003
PARP-1-Targeted Auger Emitters Display High-LET Cytotoxic Properties In Vitro but Show Limited Therapeutic Utility in Solid Tumor Models of Human Neuroblastoma. PMID:31676730
HIV Capsid Inhibitors Beyond PF74. PMID:31671622
A reaction pathway to compound 0 intermediates in oxy-myoglobin through interactions with hydrogen sulfide and His64. PMID:31670138
CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. PMID:31665441
Unraveling allosteric landscapes of allosterome with ASD. PMID:31665428
New insights into protein-DNA binding specificity from hydrogen bond based comparative study. PMID:31665426
Study of the binding mechanism of aptamer to palytoxin by docking and molecular simulation. PMID:31664144
Structural determination of Enzyme-Graphene Nanocomposite Sensor Material. PMID:31664095
Molecular Dynamics Simulations of Macromolecular Crystals. PMID:31662799
New insights into the mycobacterial PE and PPE proteins provide a framework for future research. PMID:31661176
The role of ligand-gated conformational changes in enzyme catalysis. PMID:31657438
Classification of RNA backbone conformations into rotamers using 13C' chemical shifts: exploring how far we can go. PMID:31656702
A computational study of the molecular basis of antibiotic resistance in a DXR mutant. PMID:31654265
Deleterious Variants in WNT10A, EDAR, and EDA Causing Isolated and Syndromic Tooth Agenesis: A Structural Perspective from Molecular Dynamics Simulations. PMID:31652981
Quercetin Directly Targets JAK2 and PKCδ and Prevents UV-Induced Photoaging in Human Skin. PMID:31652815
Stereoselectivity of Aldose Reductase in the Reduction of Glutathionyl-Hydroxynonanal Adduct. PMID:31652566
A Chemosensory GPCR as a Potential Target to Control the Root-Knot Nematode Meloidogyne incognita Parasitism in Plants. PMID:31652525
Effects of Hydrodynamic Interactions on the Near-Surface Diffusion of Spheroidal Molecules. PMID:31646249
Natural selection based on coordination chemistry: computational assessment of [4Fe-4S]-maquettes with non-coded amino acids. PMID:31641437
RNA 3D structure prediction guided by independent folding of homologous sequences. PMID:31640563
Bioinformatics analysis of Ras homologue enriched in the striatum, a potential target for Huntington's disease therapy. PMID:31638189
Unified rational protein engineering with sequence-based deep representation learning. PMID:31636460
Antigenic Site Variation in the Hemagglutinin of Pandemic Influenza A(H1N1)pdm09 Viruses between 2009-2017 in Ukraine. PMID:31635227
RFQAmodel: Random Forest Quality Assessment to identify a predicted protein structure in the correct fold. PMID:31634369
Genome-wide identification and expression analysis of the WRKY genes in sugar beet (Beta vulgaris L.) under alkaline stress. PMID:31632850
MemSTATS: A Benchmark Set of Membrane Protein Symmetries and Pseudosymmetries. PMID:31628944
Computational methods and tools for binding site recognition between proteins and small molecules: from classical geometrical approaches to modern machine learning strategies. PMID:31628659
Computational approaches to therapeutic antibody design: established methods and emerging trends. PMID:31626279
Computer-Assisted and Data Driven Approaches for Surveillance, Drug Discovery, and Vaccine Design for the Zika Virus. PMID:31623241
An engineered ultra-high affinity Fab-Protein G pair enables a modular antibody platform with multifunctional capability. PMID:31622515
RMSD analysis of structures of the bacterial protein FimH identifies five conformations of its lectin domain. PMID:31622514
Structural and biochemical characterisation of a novel alginate lyase from Paenibacillus sp. str. FPU-7. PMID:31619701
A structure-based approach towards the identification of novel antichagasic compounds: Trypanosoma cruzi carbonic anhydrase inhibitors. PMID:31619095
New Hydrazinothiazole Derivatives of Usnic Acid as Potent Tdp1 Inhibitors. PMID:31619021
Tuning Structure and Dynamics of Blue Copper Azurin Junctions via Single Amino-Acid Mutations. PMID:31618974
Design, synthesis, and structural elucidation of novel NmeNANAS inhibitors for the treatment of meningococcal infection. PMID:31618227
Protein structure prediction using multiple deep neural networks in the 13th Critical Assessment of Protein Structure Prediction (CASP13). PMID:31602685
ModelBricks-modules for reproducible modeling improving model annotation and provenance. PMID:31602314
TCRpMHCmodels: Structural modelling of TCR-pMHC class I complexes. PMID:31601838
Design and Selection of Novel C1s Inhibitors by In Silico and In Vitro Approaches. PMID:31600984
Cryo-EM map interpretation and protein model-building using iterative map segmentation. PMID:31599033
Macrocycle modeling in ICM: benchmarking and evaluation in D3R Grand Challenge 4. PMID:31598897
Consortia of bioactives in supercritical carbon dioxide extracts of mustard and small cardamom seeds lower serum cholesterol levels in rats: new leads for hypocholesterolaemic supplements from spices. PMID:31595188
Real-time cryo-electron microscopy data preprocessing with Warp. PMID:31591575
Topology-based classification of tetrads and quadruplex structures. PMID:31588513
Unraveling the structural and chemical features of biological short hydrogen bonds. PMID:31588321
Targeting trimeric transmembrane domain 5 of oncogenic latent membrane protein 1 using a computationally designed peptide. PMID:31588309
In vivo efficacy of mutant IDH1 inhibitor HMS-101 and structural resolution of distinct binding site. PMID:31586149
Aldehyde-alcohol dehydrogenase forms a high-order spirosome architecture critical for its activity. PMID:31586059
Reporting on the future of integrative structural biology ORAU workshop. PMID:31585877
Optimization of Protein-Ligand Electrostatic Interactions Using an Alchemical Free-Energy Method. PMID:31584802
funtrp: identifying protein positions for variation driven functional tuning. PMID:31584091
Cyclic Changes in Active Site Polarization and Dynamics Drive the 'Ping-pong' Kinetics in NRH:Quinone Oxidoreductase 2: An Insight from QM/MM Simulations. PMID:31583178
Pharmacophore Directed Screening of Agonistic Natural Molecules Showing Affinity to 5HT2C Receptor. PMID:31581577
Nitrate and Phosphate Transporters Rescue Fluoride Toxicity in Yeast. PMID:31576749
Why is interoperability between the two fields of chemical crystallography and protein crystallography so difficult? PMID:31576212
Targeting of copper-trafficking chaperones causes gene-specific systemic pathology in Drosophila melanogaster: prospective expansion of mutational landscapes that regulate tumor resistance to cisplatin. PMID:31575544
Transcriptional Bypass of DNA-Protein and DNA-Peptide Conjugates by T7 RNA Polymerase. PMID:31573793
Phage therapy as a renewed therapeutic approach to mycobacterial infections: a comprehensive review. PMID:31571947
The C-terminal dimerization domain of the respiratory mucin MUC5B functions in mucin stability and intracellular packaging before secretion. PMID:31570524
The CLN3 gene and protein: What we know. PMID:31568712
The CELLmicrocosmos Tools: A Small History of Java-Based Cell and Membrane Modelling Open Source Software Development. PMID:31560649
Genome-wide mutation analysis of Helicobacter pylori after inoculation to Mongolian gerbils. PMID:31558915
A carbohydrate-binding family 48 module enables feruloyl esterase action on polymeric arabinoxylan. PMID:31558605
Ligand-Binding-Site Structure Refinement Using Molecular Dynamics with Restraints Derived from Predicted Binding Site Templates. PMID:31557013
Blinded prediction of protein-ligand binding affinity using Amber thermodynamic integration for the 2018 D3R grand challenge 4. PMID:31555923
Thera-SAbDab: the Therapeutic Structural Antibody Database. PMID:31555805
Domain-based Comparative Analysis of Bacterial Proteomes: Uniqueness, Interactions, and the Dark Matter. PMID:31555062
Structure-Based Design and in Silico Screening of Virtual Combinatorial Library of Benzamides Inhibiting 2-trans Enoyl-Acyl Carrier Protein Reductase of Mycobacterium tuberculosis with Favorable Predicted Pharmacokinetic Profiles. PMID:31554227
Insights Into Enhanced Complement Activation by Structures of Properdin and Its Complex With the C-Terminal Domain of C3b. PMID:31552043
Distinct Chemotaxis Protein Paralogs Assemble into Chemoreceptor Signaling Arrays To Coordinate Signaling Output. PMID:31551333
Potent HIV-1 Protease Inhibitors Containing Carboxylic and Boronic Acids: Effect on Enzyme Inhibition and Antiviral Activity and Protein-Ligand X-ray Structural Studies. PMID:31549492
Mechanical Deformation and Electronic Structure of a Blue Copper Azurin in a Solid-State Junction. PMID:31546917
Identification of Functional and Druggable Sites in Aspergillus fumigatus Essential Phosphatases by Virtual Screening. PMID:31546755
Back-to-Germline (B2G) Procedure for Antibody Devolution. PMID:31544851
Phage Display Libraries for Antibody Therapeutic Discovery and Development. PMID:31544850
Computational Prediction of the Epitopes of HA1 Protein of Influenza Viruses to its Neutralizing Antibodies. PMID:31544808
Crowder-Induced Conformational Ensemble Shift in Escherichia coli Prolyl-tRNA Synthetase. PMID:31542226
Key Topics in Molecular Docking for Drug Design. PMID:31540192
Less Is More: Coarse-Grained Integrative Modeling of Large Biomolecular Assemblies with HADDOCK. PMID:31539250
Design of Gallinamide A Analogs as Potent Inhibitors of the Cysteine Proteases Human Cathepsin L and Trypanosoma cruzi Cruzain. PMID:31539239
Harnessing calcineurin-FK506-FKBP12 crystal structures from invasive fungal pathogens to develop antifungal agents. PMID:31537789
Structural characterization of EGFR exon 19 deletion mutation using molecular dynamics simulation. PMID:31536605
A novel protein descriptor for the prediction of drug binding sites. PMID:31533611
A Multi-Layered Study on Harmonic Oscillations in Mammalian Genomics and Proteomics. PMID:31533246
Molecular function limits divergent protein evolution on planetary timescales. PMID:31532392
RCSB Protein Data Bank: Enabling biomedical research and drug discovery. PMID:31531901
Enabling Web-scale data integration in biomedicine through Linked Open Data. PMID:31531395
Flow-induced mechanotransduction in skeletal cells. PMID:31529361
Intermolecular Non-Covalent Carbon-Bonding Interactions with Methyl Groups: A CSD, PDB and DFT Study. PMID:31527496
Novel Heat Shock Protein 90 Inhibitors Suppress P-Glycoprotein Activity and Overcome Multidrug Resistance in Cancer Cells. PMID:31527404
Predicting and Experimentally Validating Hot-Spot Residues at Protein-Protein Interfaces. PMID:31525028
Predicting Sequence Features, Function, and Structure of Proteins Using MESSA. PMID:31524991
HH-suite3 for fast remote homology detection and deep protein annotation. PMID:31521110
Illustrate: Software for Biomolecular Illustration. PMID:31519398
Improved Modeling of Cation-π and Anion-Ring Interactions Using the Drude Polarizable Empirical Force Field for Proteins. PMID:31518010
Effect of piceatannol-rich passion fruit seed extract on human glyoxalase I-mediated cancer cell growth. PMID:31517069
Computational characterization of the glutamate receptor antagonist perampanel and its close analogs: density functional exploration of conformational space and molecular docking study. PMID:31511986
Improved deep learning-based macromolecules structure classification from electron cryo-tomograms. PMID:31511756
Computational chemoproteomics to understand the role of selected psychoactives in treating mental health indications. PMID:31511563
Multifaceted protein-protein interaction prediction based on Siamese residual RCNN. PMID:31510705
Precise modelling and interpretation of bioactivities of ligands targeting G protein-coupled receptors. PMID:31510691
SCRIBER: accurate and partner type-specific prediction of protein-binding residues from proteins sequences. PMID:31510679
Adversarial domain adaptation for cross data source macromolecule in situ structural classification in cellular electron cryo-tomograms. PMID:31510673
Uncovering the Role of Key Active-Site Side Chains in Catalysis: An Extended Brønsted Relationship for Substrate Deprotonation Catalyzed by Wild-Type and Variants of Triosephosphate Isomerase. PMID:31508957
Docking Flexible Cyclic Peptides with AutoDock CrankPep. PMID:31505931
Different Synergy in Amyloids and Biologically Active Forms of Proteins. PMID:31505841
WALTZ-DB 2.0: an updated database containing structural information of experimentally determined amyloid-forming peptides. PMID:31504823
Stereospecificity control in aminoacyl-tRNA-synthetases: new evidence of d-amino acids activation and editing. PMID:31504788
MHC binding affects the dynamics of different T-cell receptors in different ways. PMID:31498801
Data-Driven Construction of Antitumor Agents with Controlled Polypharmacology. PMID:31497954
Exploring Novel N-Myristoyltransferase Inhibitors: A Molecular Dynamics Simulation Approach. PMID:31497683
Thermal Stability of Peptide Nucleic Acid Complexes. PMID:31491077
A Fragmenting Protocol with Explicit Hydration for Calculation of Binding Enthalpies of Target-Ligand Complexes at a Quantum Mechanical Level. PMID:31489952
Using parallelized incremental meta-docking can solve the conformational sampling issue when docking large ligands to proteins. PMID:31488048
Molecular Docking: Shifting Paradigms in Drug Discovery. PMID:31487867
Molecular Dynamics Gives New Insights into the Glucose Tolerance and Inhibition Mechanisms on β-Glucosidases. PMID:31487855
EPHA2 mutations with oncogenic characteristics in squamous cell lung cancer and malignant pleural mesothelioma. PMID:31484920
Independent evolution of rosmarinic acid biosynthesis in two sister families under the Lamiids clade of flowering plants. PMID:31481469
Selenocysteine β-Lyase: Biochemistry, Regulation and Physiological Role of the Selenocysteine Decomposition Enzyme. PMID:31480609
Intestinal serotonin and fluoxetine exposure modulate bacterial colonization in the gut. PMID:31477894
A Structure-Informed Atlas of Human-Virus Interactions. PMID:31474372
GPT2 mutations in autosomal recessive developmental disability: extending the clinical phenotype and population prevalence estimates. PMID:31471722
A Novel Homozygous Missense Variant in the NAGA Gene with Extreme Intrafamilial Phenotypic Heterogeneity. PMID:31468281
Is radiation damage the limiting factor in high-resolution single particle imaging with X-ray free-electron lasers? PMID:31463335
Comparative in silico study of congocidine congeners as potential inhibitors of African swine fever virus. PMID:31461446
Predicting Monovalent Ion Correlation Effects in Nucleic Acids. PMID:31460472
Insights to the Assembly of a Functionally Active Leptospiral ClpP1P2 Protease Complex along with Its ATPase Chaperone ClpX. PMID:31460415
Portrait of the Intrinsically Disordered Side of the HTLV-1 Proteome. PMID:31460093
Large-Scale Target Identification of Herbal Medicine Using a Reverse Docking Approach. PMID:31460061
Simple Coordination Geometry Descriptors Allow to Accurately Predict Metal-Binding Sites in Proteins. PMID:31459585
Promiscuous Ligands from Experimentally Determined Structures, Binding Conformations, and Protein Family-Dependent Interaction Hotspots. PMID:31459430
A Diverse Benchmark Based on 3D Matched Molecular Pairs for Validating Scoring Functions. PMID:31458770
Structural Insights from Molecular Dynamics Simulations of Tryptophan 7-Halogenase and Tryptophan 5-Halogenase. PMID:31458701
Prediction of Accurate Binding Modes Using Combination of Classical and Accelerated Molecular Dynamics and Free-Energy Perturbation Calculations: An Application to Toxicity Studies. PMID:31458661
Coupled Mutations-Enabled Glycerol Transportation in an Aquaporin Z Mutant. PMID:31458647
Promiscuous Ligands from Experimentally Determined Structures, Binding Conformations, and Protein Family-Dependent Interaction Hotspots. PMID:31459430
A Diverse Benchmark Based on 3D Matched Molecular Pairs for Validating Scoring Functions. PMID:31458770
Structural Insights from Molecular Dynamics Simulations of Tryptophan 7-Halogenase and Tryptophan 5-Halogenase. PMID:31458701
Prediction of Accurate Binding Modes Using Combination of Classical and Accelerated Molecular Dynamics and Free-Energy Perturbation Calculations: An Application to Toxicity Studies. PMID:31458661
Coupled Mutations-Enabled Glycerol Transportation in an Aquaporin Z Mutant. PMID:31458647
Charge-Transfer Knowledge Graph among Amino Acids Derived from High-Throughput Electronic Structure Calculations for Protein Database. PMID:31458645
Insights into the ZIKV NS1 Virology from Different Strains through a Fine Analysis of Physicochemical Properties. PMID:31458257
Characterization of Ionizable Groups' Environments in Proteins and Protein-Ligand Complexes through a Statistical Analysis of the Protein Data Bank. PMID:31457307
Modelling of substrate access and substrate binding to cephalosporin acylases. PMID:31455800
The role of structural pleiotropy and regulatory evolution in the retention of heteromers of paralogs. PMID:31454312
π-Hole Interactions Involving Nitro Aromatic Ligands in Protein Structures. PMID:31453653
Deeper Profiles and Cascaded Recurrent and Convolutional Neural Networks for state-of-the-art Protein Secondary Structure Prediction. PMID:31451723
Next-Generation Noncompetitive Nanosystems Based on Gambogic Acid: In silico Identification of Transferrin Receptor Binding Sites, Regulatory Shelf Stability, and Their Preliminary Safety in Healthy Rodents. PMID:31440745
Specialized structural and functional roles of residues selectively conserved in subfamilies of the pleckstrin homology domain family. PMID:31436855
Insights from the salt bridge analysis of malate dehydrogenase from H. salinarum and E.coli. PMID:31435155
Deciphering the Molecular Recognition Mechanism of Multidrug Resistance Staphylococcus aureus NorA Efflux Pump Using a Supervised Molecular Dynamics Approach. PMID:31430864
Hidden bias in the DUD-E dataset leads to misleading performance of deep learning in structure-based virtual screening. PMID:31430292
Comprehensive classification of the plant non-specific lipid transfer protein superfamily towards its sequence-structure-function analysis. PMID:31428542
PredPRBA: Prediction of Protein-RNA Binding Affinity Using Gradient Boosted Regression Trees. PMID:31428122
A comprehensive computational study of amino acid interactions in membrane proteins. PMID:31427701
Encapsulation of Aspartic Protease in Nonlamellar Lipid Liquid Crystalline Phases. PMID:31422820
Benzo[b]tiophen-3-ol derivatives as effective inhibitors of human monoamine oxidase: design, synthesis, and biological activity. PMID:31422706
Molecular modeling of four Dermaseptin-related peptides of the gliding tree frog Agalychnis spurrelli. PMID:31422479
Advances in protein structure prediction and design. PMID:31417196
Identification of the active site residues in ATP-citrate lyase's carboxy-terminal portion. PMID:31411782
The ABCD database: a repository for chemically defined antibodies. PMID:31410491
New CXCR1/CXCR2 inhibitors represent an effective treatment for kidney or head and neck cancers sensitive or refractory to reference treatments. PMID:31410218
Systematic FTIR Spectroscopy Study of the Secondary Structure Changes in Human Serum Albumin under Various Denaturation Conditions. PMID:31409012
Cyclodextrins Can Entrap Zearalenone-14-Glucoside: Interaction of the Masked Mycotoxin with Cyclodextrins and Cyclodextrin Bead Polymer. PMID:31405003
De Novo Missense Variants in FBXW11 Cause Diverse Developmental Phenotypes Including Brain, Eye, and Digit Anomalies. PMID:31402090
Computational Insights into Avidity of Polymeric Multivalent Binders. PMID:31400918
Nascent Polypeptide Domain Topology and Elongation Rate Direct the Cotranslational Hierarchy of Hsp70 and TRiC/CCT. PMID:31400849
PUG-View: programmatic access to chemical annotations integrated in PubChem. PMID:31399858
Computational Assessment of Bacterial Protein Structures Indicates a Selection Against Aggregation. PMID:31398930
Investigation of the effect of UV-B light on Arabidopsis MYB4 (AtMYB4) transcription factor stability and detection of a putative MYB4-binding motif in the promoter proximal region of AtMYB4. PMID:31393961
Pyrazolo[4,3-e][1,2,4]triazolo[1,5-c]pyrimidines to develop functionalized ligands to target adenosine receptors: fluorescent ligands as an example. PMID:31391881
Isoform-Specific Destabilization of the Active Site Reveals a Molecular Mechanism of Intrinsic Activation of KRas G13D. PMID:31390567
Identification of potential binding pocket on viral oncoprotein HPV16 E6: a promising anti-cancer target for small molecule drug discovery. PMID:31387520
Bioinformatics classification of mutations in patients with Mucopolysaccharidosis IIIA. PMID:31385193
Antimicrobial, antioxidant and cytotoxic evaluation of diazenyl chalcones along with insights to mechanism of interaction by molecular docking studies. PMID:31384834
α-Glucosidase inhibitors from a mangrove associated fungus, Zasmidium sp. strain EM5-10. PMID:31384771
Reduced Function and Diversity of T Cell Repertoire and Distinct Clinical Course in Patients With IL7RA Mutation. PMID:31379863
In silico design and optimization of selective membranolytic anticancer peptides. PMID:31375699
Sequence-dependent RNA helix conformational preferences predictably impact tertiary structure formation. PMID:31375637
Antibacterial Activity and Molecular Docking Studies of a Selected Series of Hydroxy-3-arylcoumarins. PMID:31375003
Sequence assignment for low-resolution modelling of protein crystal structures. PMID:31373574
Fast, efficient fragment-based coordinate generation for Open Babel. PMID:31372768
A hybrid, bottom-up, structurally accurate, Go¯-like coarse-grained protein model. PMID:31370551
Missense mutations in the C-terminal portion of the B4GALNT2-encoded glycosyltransferase underlying the Sd(a-) phenotype. PMID:31367682
Effects of the Q80K Polymorphism on the Physicochemical Properties of Hepatitis C Virus Subtype 1a NS3 Protease. PMID:31366046
Revisiting the Allosteric Regulation of Sodium Cation on the Binding of Adenosine at the Human A2A Adenosine Receptor: Insights from Supervised Molecular Dynamics (SuMD) Simulations. PMID:31362426
Adaptations for Pressure and Temperature Effects on Loop Motion in Escherichia coli and Moritella profunda Dihydrofolate Reductase. PMID:31359910
Protein secondary structure detection in intermediate-resolution cryo-EM maps using deep learning. PMID:31358979
Peptide-Protein Interaction Studies of Antimicrobial Peptides Targeting Middle East Respiratory Syndrome Coronavirus Spike Protein: An In Silico Approach. PMID:31354813
Analysis of salt-bridges in prolyl oligopeptidase from Pyrococcus furiosus and Homo sapiens. PMID:31354198
NMR-assisted protein structure prediction with MELDxMD. PMID:31350773
Elevated neoantigen levels in tumors with somatic mutations in the HLA-A, HLA-B, HLA-C and B2M genes. PMID:31345234
Rational design of an XNA ligase through docking of unbound nucleic acids to toroidal proteins. PMID:31334814
Exploring Wells-Dawson Clusters Associated With the Small Ribosomal Subunit. PMID:31334216
Insights about multi-targeting and synergistic neuromodulators in Ayurvedic herbs against epilepsy: integrated computational studies on drug-target and protein-protein interaction networks. PMID:31332210
Multiscale Molecular Dynamics Simulation of Multiple Protein Adsorption on Gold Nanoparticles. PMID:31331044
Can We Still Trust Docking Results? An Extension of the Applicability of DockBench on PDBbind Database. PMID:31330841
Organization of Farnesylated, Carboxymethylated KRAS4B on Membranes. PMID:31330153
Structural Insights into Hearing Loss Genetics from Polarizable Protein Repacking. PMID:31327459
Comparative structural and thermal stability studies of Cuc m 2.0101, Art v 4.0101 and other allergenic profilins. PMID:31326654
High Functioning Autism with Missense Mutations in Synaptotagmin-Like Protein 4 (SYTL4) and Transmembrane Protein 187 (TMEM187) Genes: SYTL4- Protein Modeling, Protein-Protein Interaction, Expression Profiling and MicroRNA Studies. PMID:31323913
FunFam protein families improve residue level molecular function prediction. PMID:31319797
Hydrogen Bond Enhanced Halogen Bonds: A Synergistic Interaction in Chemistry and Biochemistry. PMID:31318520
IRAM: virus capsid database and analysis resource. PMID:31318422
A newly developed anesthetic based on a unique chemical core. PMID:31308218
Benchmarking subcellular localization and variant tolerance predictors on membrane proteins. PMID:31307390
Identification of Intrinsically Disordered Proteins and Regions by Length-Dependent Predictors Based on Conditional Random Fields. PMID:31307006
Acetaminophen Overdose as a Potential Risk Factor for Parkinson's Disease. PMID:31305025
Umbrella Visualization: A method of analysis dedicated to glycan flexibility with UnityMol. PMID:31302178
The mechanism of RNA duplex recognition and unwinding by DEAD-box helicase DDX3X. PMID:31300642
An NMR and MD study of complexes of bacteriophage lambda lysozyme with tetra- and hexa-N-acetylchitohexaose. PMID:31294851
The influence of water potential in simulation: a catabolite activator protein case study. PMID:31292786
Prediction of disease-associated mutations in the transmembrane regions of proteins with known 3D structure. PMID:31291347
MemBlob database and server for identifying transmembrane regions using cryo-EM maps. PMID:31290936
Getting Docking into Shape Using Negative Image-Based Rescoring. PMID:31290660
Coarse-grain simulations on NMR conformational ensembles highlight functional residues in proteins. PMID:31288649
Screening of caspase-3 inhibitors from natural molecule database using e-pharmacophore and docking studies. PMID:31285640
NU-6027 Inhibits Growth of Mycobacterium tuberculosis by Targeting Protein Kinase D and Protein Kinase G. PMID:31285226
Archiving and disseminating integrative structure models. PMID:31278630
Structural knowledge or X-ray damage? A case study on xylose isomerase illustrating both. PMID:31274415
Kinase Atlas: Druggability Analysis of Potential Allosteric Sites in Kinases. PMID:31274316
Extensive benchmark of rDock as a peptide-protein docking tool. PMID:31270654
Exploring the dark genome: implications for precision medicine. PMID:31270560
Crystal Structure of Phosphoserine BlaC from Mycobacterium tuberculosis Inactivated by Bis(Benzoyl) Phosphate. PMID:31269656
Prediction of an Upper Limit for the Fraction of Interprotein Cross-Links in Large-Scale In Vivo Cross-Linking Studies. PMID:31267744
Modulating Integrin αIIbβ3 Activity through Mutagenesis of Allosterically Regulated Intersubunit Contacts. PMID:31264850
A Ligand-Based Virtual Screening Method Using Direct Quantification of Generalization Ability. PMID:31262005
Biochemical Characterization of a Novel Monospecific Endo-β-1,4-Glucanase Belonging to GH Family 5 From a Rhizosphere Metagenomic Library. PMID:31258522
Continuous Evaluation of Ligand Protein Predictions: A Weekly Community Challenge for Drug Docking. PMID:31257108
A non-beta-lactam antibiotic inhibitor for enterohemorrhagic Escherichia coli O104:H4. PMID:31254005
A genetics-led approach defines the drug target landscape of 30 immune-related traits. PMID:31253980
The structure-activity profile of mercaptobenzamides' anti-HIV activity suggests that thermodynamics of metabolism is more important than binding affinity to the target. PMID:31252286
The PSIPRED Protein Analysis Workbench: 20 years on. PMID:31251384
MolMeDB: Molecules on Membranes Database. PMID:31250015
Fold combinations in multi-domain proteins. PMID:31249437
MPLs-Pred: Predicting Membrane Protein-Ligand Binding Sites Using Hybrid Sequence-Based Features and Ligand-Specific Models. PMID:31247932
Comparative Exploratory Analysis of Intrinsically Disordered Protein Dynamics Using Machine Learning and Network Analytic Methods. PMID:31245383
Structural Analysis and Conformational Dynamics of STN1 Gene Mutations Involved in Coat Plus Syndrome. PMID:31245382
Development of Allosteric BRAF Peptide Inhibitors Targeting the Dimer Interface of BRAF. PMID:31243962
Identification of Extracellular DNA-Binding Proteins in the Biofilm Matrix. PMID:31239382
Ligand-guided homology modeling drives identification of novel histamine H3 receptor ligands. PMID:31237914
QSAR Classification Models for Predicting the Activity of Inhibitors of Beta-Secretase (BACE1) Associated with Alzheimer's Disease. PMID:31235739
Searching the Optimal Folding Routes of a Complex Lasso Protein. PMID:31235180
In Silico Insights into HIV-1 Vpu-Tetherin Interactions and Its Mutational Counterparts. PMID:31234536
Abundance of HPV L1 Intra-Genotype Variants With Capsid Epitopic Modifications Found Within Low- and High-Grade Pap Smears With Potential Implications for Vaccinology. PMID:31231420
Gene-specific features enhance interpretation of mutational impact on acid α-glucosidase enzyme activity. PMID:31228295
Deep sequencing of 2009 influenza A/H1N1 virus isolated from volunteer human challenge study participants and natural infections. PMID:31226666
The human endogenous metabolome as a pharmacology baseline for drug discovery. PMID:31226432
Virtual screening and docking of lead like molecules against Glutathione-S-Transferase protein from Brugia malayi. PMID:31223214
Antiproliferative Benzoindazolequinones as Potential Cyclooxygenase-2 Inhibitors. PMID:31216654
Metal-Biosurfactant Complexes Characterization: Binding, Self-Assembly and Interaction with Bovine Serum Albumin. PMID:31212764
Fitness of unregulated human Ras mutants modeled by implementing computational mutagenesis and machine learning techniques. PMID:31211262
Mapping Spatiotemporal Microproteomics Landscape in Experimental Model of Traumatic Brain Injury Unveils a link to Parkinson's Disease. PMID:31204315
Rational creation and systematic analysis of cervical cancer kinase-inhibitor binding profile. PMID:31203490
Clinical, biochemical and genetic profiles of patients with mucopolysaccharidosis type IVA (Morquio A syndrome) in Malaysia: the first national natural history cohort study. PMID:31200731
DeepConv-DTI: Prediction of drug-target interactions via deep learning with convolution on protein sequences. PMID:31199797
Decrypting protein surfaces by combining evolution, geometry, and molecular docking. PMID:31199528
Entry modes of ellipsoidal nanoparticles on a membrane during clathrin-mediated endocytosis. PMID:31190048
Why Some Targets Benefit from beyond Rule of Five Drugs. PMID:31188592
Dissecting macromolecular recognition sites in ribosome: implication to its self-assembly. PMID:31179876
Dissecting the mechanisms of cell division. PMID:31175154
The Role of a Key Amino Acid Position in Species-Specific Proteinaceous dUTPase Inhibition. PMID:31174420
A Practical Perspective: The Effect of Ligand Conformers on the Negative Image-Based Screening. PMID:31174295
Protein contact prediction using metagenome sequence data and residual neural networks. PMID:31173061
Improved algorithms for quantifying the near symmetry of proteins: complete side chains analysis. PMID:31172379
The breadth of HIV-1 neutralizing antibodies depends on the conservation of key sites in their epitopes. PMID:31170145
Exploring the overlapping binding sites of ifenprodil and EVT-101 in GluN2B-containing NMDA receptors using novel chicken embryo forebrain cultures and molecular modeling. PMID:31164987
Identifying the molecular target sites for CFTR potentiators GLPG1837 and VX-770. PMID:31164398
AutoDock CrankPep: combining folding and docking to predict protein-peptide complexes. PMID:31161213
PRISMOID: a comprehensive 3D structure database for post-translational modifications and mutations with functional impact. PMID:31161204
A case of Coffin-Siris syndrome with severe congenital heart disease and a novel SMARCA4 variant. PMID:31160358
The pneumococcal σX activator, ComW, is a DNA-binding protein critical for natural transformation. PMID:31160340
ANDIS: an atomic angle- and distance-dependent statistical potential for protein structure quality assessment. PMID:31159742
Stochastic modeling of nanoparticle internalization and expulsion through receptor-mediated transcytosis. PMID:31157808
Structure, Function, and Dynamics of the Gα Binding Domain of Ric-8A. PMID:31155309
Inaccurate secondary structure predictions often indicate protein fold switching. PMID:31148305
Heterogeneous Dielectric Implicit Membrane Model for the Calculation of MMPBSA Binding Free Energies. PMID:31145610
Recent advances in understanding the replication initiator protein of the ssDNA plant viruses of the family Nanoviridae. PMID:31143829
Predicting Molecular Energy Using Force-Field Optimized Geometries and Atomic Vector Representations Learned from an Improved Deep Tensor Neural Network. PMID:31142110
Klebsiella pneumoniae O1 and O2ac antigens provide prototypes for an unusual strategy for polysaccharide antigen diversification. PMID:31138653
Genome-Wide Identification of Na+/H+ Antiporter (NHX) Genes in Sugar Beet (Beta vulgaris L.) and Their Regulated Expression under Salt Stress. PMID:31137880
Kalium 2.0, a comprehensive database of polypeptide ligands of potassium channels. PMID:31133708
Target identification, screening and in vivo evaluation of pyrrolone-fused benzosuberene compounds against human epilepsy using Zebrafish model of pentylenetetrazol-induced seizures. PMID:31133639
Gypsum-DL: an open-source program for preparing small-molecule libraries for structure-based virtual screening. PMID:31127411
Mosaic origin of the eukaryotic kinetochore. PMID:31127038
Updates to Binding MOAD (Mother of All Databases): Polypharmacology Tools and Their Utility in Drug Repurposing. PMID:31125569
Exploration of the TRIM Fold of MuRF1 Using EPR Reveals a Canonical Antiparallel Structure and Extended COS-Box. PMID:31125568
Structural analysis of Cytochrome P450 BM3 mutant M11 in complex with dithiothreitol. PMID:31125381
Leishmania infantum arginase: biochemical characterization and inhibition by naturally occurring phenolic substances. PMID:31124384
A benchmark study of loop modeling methods applied to G protein-coupled receptors. PMID:31123958
Computational Screening and Analysis of Lung Cancer Related Non-Synonymous Single Nucleotide Polymorphisms on the Human Kirsten Rat Sarcoma Gene. PMID:31117243
Fragment-Based Ligand-Protein Contact Statistics: Application to Docking Simulations. PMID:31117183
Bayesian optimization for conformer generation. PMID:31115707
SEPPA 3.0-enhanced spatial epitope prediction enabling glycoprotein antigens. PMID:31114919
HNADOCK: a nucleic acid docking server for modeling RNA/DNA-RNA/DNA 3D complex structures. PMID:31114906
2StrucCompare: a webserver for visualizing small but noteworthy differences between protein tertiary structures through interrogation of the secondary structure content. PMID:31114904
mCSM-PPI2: predicting the effects of mutations on protein-protein interactions. PMID:31114883
PrankWeb: a web server for ligand binding site prediction and visualization. PMID:31114880
DaReUS-Loop: a web server to model multiple loops in homology models. PMID:31114872
Structural and mutational analyses of psychrophilic and mesophilic adenylate kinases highlight the role of hydrophobic interactions in protein thermal stability. PMID:31111079
A Functional Agonist of Insect Olfactory Receptors: Behavior, Physiology and Structure. PMID:31110474
Limits in accuracy and a strategy of RNA structure prediction using experimental information. PMID:31106330
MERMAID: dedicated web server to prepare and run coarse-grained membrane protein dynamics. PMID:31106328
A Recurrent Missense Variant in AP2M1 Impairs Clathrin-Mediated Endocytosis and Causes Developmental and Epileptic Encephalopathy. PMID:31104773
DNA Conformational Changes Play a Force-Generating Role during Bacteriophage Genome Packaging. PMID:31103227
CRB1-Related Leber Congenital Amaurosis: Reporting Novel Pathogenic Variants and a Brief Review on Mutations Spectrum. PMID:31103025
Geometric description of self-interaction potential in symmetric protein complexes. PMID:31101822
Structural and free energy landscape of novel mutations in ribosomal protein S1 (rpsA) associated with pyrazinamide resistance. PMID:31097767
Protein Melting Temperature Cannot Fully Assess Whether Protein Folding Free Energy Underlies the Universal Abundance-Evolutionary Rate Correlation Seen in Proteins. PMID:31093676
Translation of yes-associated protein (YAP) was antagonized by its circular RNA via suppressing the assembly of the translation initiation machinery. PMID:31092884
Oxidative opening of the aromatic ring: Tracing the natural history of a large superfamily of dioxygenase domains and their relatives. PMID:31092555
Structural studies of antiviral inhibitor with HIV-1 protease bearing drug resistant substitutions of V32I, I47V and V82I. PMID:31092330
rstoolbox - a Python library for large-scale analysis of computational protein design data and structural bioinformatics. PMID:31092198
A Comprehensive Review on Current Advances in Peptide Drug Development and Design. PMID:31091705
Design and Characterization of Protein E-PilA, a Candidate Fusion Antigen for Nontypeable Haemophilus influenzae Vaccine. PMID:31085711
Methods for the Refinement of Protein Structure 3D Models. PMID:31075942
Molecular modeling studies on the interactions of 7-methoxytacrine-4-pyridinealdoxime, 4-PA, 2-PAM, and obidoxime with VX-inhibited human acetylcholinesterase: a near attack conformation approach. PMID:31074292
VoroMQA web server for assessing three-dimensional structures of proteins and protein complexes. PMID:31073605
Prediction and characterisation of lantibiotic structures with molecular modelling and molecular dynamics simulations. PMID:31073133
Surface patches on recombinant erythropoietin predict protein solubility: engineering proteins to minimise aggregation. PMID:31072369
SPADE web service for prediction of allergen IgE epitopes. PMID:31066444
From GROMACS to LAMMPS: GRO2LAM : A converter for molecular dynamics software. PMID:31065808
A deep learning approach to the structural analysis of proteins. PMID:31065348
Characterization of a Unique Form of Arrhythmic Cardiomyopathy Caused by Recessive Mutation in LEMD2. PMID:31061923
Atomic Motif Recognition in (Bio)Polymers: Benchmarks From the Protein Data Bank. PMID:31058166
Germline Predisposition and Copy Number Alteration in Pre-stage Lung Adenocarcinomas Presenting as Ground-Glass Nodules. PMID:31058088
An Overview of Molecular Modeling for Drug Discovery with Specific Illustrative Examples of Applications. PMID:31052253
High precision protein functional site detection using 3D convolutional neural networks. PMID:31051039
Maximizing accuracy of RNA structure in refinement against residual dipolar couplings. PMID:31049778
Novel choline analog 2-(4-((1-phenyl-1H-pyrazol-4-yl)methyl)piperazin-1-yl)ethan-1-ol produces sympathoinhibition, hypotension, and antihypertensive effects. PMID:31049606
Ten quick tips for using a Raspberry Pi. PMID:31048834
Chemical shift-based methods in NMR structure determination. PMID:31047599
IntFOLD: an integrated web resource for high performance protein structure and function prediction. PMID:31045208
Configurational Entropy Components and Their Contribution to Biomolecular Complex Formation. PMID:31042036
Control of anterior GRadient 2 (AGR2) dimerization links endoplasmic reticulum proteostasis to inflammation. PMID:31040128
Insights into an alternative benzofuran binding mode and novel scaffolds of polyketide synthase 13 inhibitors. PMID:31025202
Rosmarinic Acid Attenuates Cadmium-Induced Nephrotoxicity via Inhibition of Oxidative Stress, Apoptosis, Inflammation and Fibrosis. PMID:31022990
An Open Science Approach to Artificial Intelligence in Healthcare. PMID:31022753
AbRSA: A robust tool for antibody numbering. PMID:31020723
Structural basis of ligand recognition at the human MT1 melatonin receptor. PMID:31019306
Protein interaction disruption in cancer. PMID:31014259
Detailed prediction of protein sub-nuclear localization. PMID:31014229
Prevention of Deficit in Neuropsychiatric Disorders through Monitoring of Arsenic and Its Derivatives as Well as Through Bioinformatics and Cheminformatics. PMID:31013686
Design and Synthesis of Selective Phosphodiesterase 4D (PDE4D) Allosteric Inhibitors for the Treatment of Fragile X Syndrome and Other Brain Disorders. PMID:31013090
Structure-Activity Relationship of NF023 Derivatives Binding to XIAP-BIR1. PMID:31011505
Flexible Backbone Assembly and Refinement of Symmetrical Homomeric Complexes. PMID:31006588
The Relevance of Glutathione Reductase Inhibition by Fluoxetine to Human Health and Disease: Insights Derived from a Combined Kinetic and Docking Study. PMID:31004256
Framework for Conducting and Analyzing Crystal Simulations of Nucleic Acids to Aid in Modern Force Field Evaluation. PMID:31002511
Structures and functions linked to genome-wide adaptation of human influenza A viruses. PMID:31000776
Forging tools for refining predicted protein structures. PMID:31000596
EvolStruct-Phogly: incorporating structural properties and evolutionary information from profile bigrams for the phosphoglycerylation prediction. PMID:30999859
Influence of multiple-sequence-alignment depth on Potts statistical models of protein covariation. PMID:30999494
Insights into the Molecular Mechanisms of Eg5 Inhibition by (+)-Morelloflavone. PMID:30995725
Epigenetic Modulators as Potential Multi-targeted Drugs Against Hedgehog Pathway for Treatment of Cancer. PMID:30993446
Analysis of tractable allosteric sites in G protein-coupled receptors. PMID:30992500
Evaluating the performance of MM/PBSA for binding affinity prediction using class A GPCR crystal structures. PMID:30989574
Exascale Computing: A New Dawn for Computational Biology. PMID:30983889
Evidence for ligandable sites in structured RNA throughout the Protein Data Bank. PMID:30982658
Substance P in the Gas Phase: Conformational Changes and Dissociations Induced by Collisional Activation in a Drift Tube. PMID:30980379
MoleGear: A Java-Based Platform for Evolutionary De Novo Molecular Design. PMID:30979097
Study of correlations between protein peptide plane dynamics and side chain dynamics. PMID:30978222
A global map of the protein shape universe. PMID:30978181
Negative Regulation of the Mis17-Mis6 Centromere Complex by mRNA Decay Pathway and EKC/KEOPS Complex in Schizosaccharomyces pombe. PMID:30967422
Topological Models for Open-Knotted Protein Chains Using the Concepts of Knotoids and Bonded Knotoids. PMID:30965745
TeachOpenCADD: a teaching platform for computer-aided drug design using open source packages and data. PMID:30963287
RMalign: an RNA structural alignment tool based on a novel scoring function RMscore. PMID:30961545
Structure and Dynamics of the EGF Receptor as Revealed by Experiments and Simulations and Its Relevance to Non-Small Cell Lung Cancer. PMID:30959819
In Silico Peptide Ligation: Iterative Residue Docking and Linking as a New Approach to Predict Protein-Peptide Interactions. PMID:30959812
New Zealand Tree and Giant Wētā (Orthoptera) Transcriptomics Reveal Divergent Selection Patterns in Metabolic Loci. PMID:30957857
Recognition of repulsive and attractive regions of selected serotonin receptor binding site using FMO-EDA approach. PMID:30955095
Metabolism of the dual FLT-3/Aurora kinase inhibitor CCT241736 in preclinical and human in vitro models: Implication for the choice of toxicology species. PMID:30953752
How to benchmark RNA secondary structure prediction accuracy. PMID:30951834
MedusaDock 2.0: Efficient and Accurate Protein-Ligand Docking With Constraints. PMID:30946779
Adaptations of Alteromonas sp. 76-1 to Polysaccharide Degradation: A CAZyme Plasmid for Ulvan Degradation and Two Alginolytic Systems. PMID:30936857
A small-molecule inhibitor of the DNA recombinase Rad51 from Plasmodium falciparum synergizes with the antimalarial drugs artemisinin and chloroquine. PMID:30936202
Dark Proteome Database: Studies on Dark Proteins. PMID:30934744
Molecular Docking and Dynamics Simulation Studies Predict Munc18b as a Target of Mycolactone: A Plausible Mechanism for Granule Exocytosis Impairment in Buruli Ulcer Pathogenesis. PMID:30934618
pH-induced morphological changes of proteinaceous viral shells. PMID:30926857
Inhibition of Oncogenic Kinases: An In Vitro Validated Computational Approach Identified Potential Multi-Target Anticancer Compounds. PMID:30925835
Role of Structural Features in Oligomerization, Active-Site Integrity and Ligand Binding of Ribose-1,5-Bisphosphate Isomerase. PMID:30923607
Estimating probabilistic context-free grammars for proteins using contact map constraints. PMID:30918754
Copper(II) complexes as potential anticancer and Nonsteroidal anti-inflammatory agents: In vitro and in vivo studies. PMID:30918270
Deep Learning for Validating and Estimating Resolution of Cryo-Electron Microscopy Density Maps †. PMID:30917528
a-ARM: Automatic Rhodopsin Modeling with Chromophore Cavity Generation, Ionization State Selection, and External Counterion Placement. PMID:30916955
Anticipating innovations in structural biology. PMID:30912485
Novel compound mutations in the mitochondrial translation elongation factor (TSFM) gene cause severe cardiomyopathy with myocardial fibro-adipose replacement. PMID:30911037
Position 123 of halohydrin dehalogenase HheG plays an important role in stability, activity, and enantioselectivity. PMID:30911023
Electrostatics of Tau Protein by Molecular Dynamics. PMID:30909607
Effects of Pressure and Temperature on the Atomic Fluctuations of Dihydrofolate Reductase from a Psychropiezophile and a Mesophile. PMID:30909394
Predicting Protein Dimer Structures Using MELD × MD. PMID:30908034
Structural investigation of Rett-inducing MeCP2 mutations. PMID:30906830
Structure-based identification of potent VEGFR-2 inhibitors from in vivo metabolites of a herbal ingredient. PMID:30904971
The role of ABCA7 in Alzheimer's disease: evidence from genomics, transcriptomics and methylomics. PMID:30903345
Binding mode information improves fragment docking. PMID:30903304
Differential proteostatic regulation of insoluble and abundant proteins. PMID:30903148
Rapid interpretation of small-angle X-ray scattering data. PMID:30901335
A comprehensive in silico analysis of sortase superfamily. PMID:30900148
The exonuclease Xrn1 activates transcription and translation of mRNAs encoding membrane proteins. PMID:30899024
QRNAS: software tool for refinement of nucleic acid structures. PMID:30898165
Structure-Activity Relationship of Purine and Pyrimidine Nucleotides as Ecto-5'-Nucleotidase (CD73) Inhibitors. PMID:30895781
The Light and Dark Sides of Virtual Screening: What Is There to Know? PMID:30893780
Identification of a α-helical molten globule intermediate and structural characterization of β-cardiotoxin, an all β-sheet protein isolated from the venom of Ophiophagus hannah (king cobra). PMID:30891862
Modifying inter-cistronic sequence significantly enhances IRES dependent second gene expression in bicistronic vector: Construction of optimised cassette for gene therapy of familial hypercholesterolemia. PMID:30891532
Elucidating the druggability of the human proteome with eFindSite. PMID:30888556
Understanding Effects of PAMAM Dendrimer Size and Surface Chemistry on Serum Protein Binding with Discrete Molecular Dynamics Simulations. PMID:30881771
Predicting protein-ligand binding affinity and correcting crystal structures with quantum mechanical calculations: lactate dehydrogenase A. PMID:30881647
An Improved Deep Forest Model for Predicting Self-Interacting Proteins From Protein Sequence Using Wavelet Transformation. PMID:30881376
Drug-release system of microchannel transport used in minimally invasive surgery for hemostasis. PMID:30880920
The Balancing Act of Intrinsically Disordered Proteins: Enabling Functional Diversity while Minimizing Promiscuity. PMID:30878482
In Silico Analysis of Homologous Heterodimers of Cruzipain-Chagasin from Structural Models Built by Homology. PMID:30875920
Adenosine Induces EBV Lytic Reactivation through ADORA1 in EBV-Associated Gastric Carcinoma. PMID:30875759
Fragment Hits: What do They Look Like and How do They Bind? PMID:30875465
Predicting protein residue-residue contacts using random forests and deep networks. PMID:30871477
HCV Pit Stop at the Lipid Droplet: Refuel Lipids and Put on a Lipoprotein Coat before Exit. PMID:30871009
Dynamic analysis of human tyrosinase intra-melanosomal domain and mutant variants to further understand oculocutaneous albinism type 1. PMID:30868138
Quantum chemical calculation and binding modes of H1R; a combined study of molecular docking and DFT for suggesting therapeutically potent H1R antagonist. PMID:30863716
Unraveling RNA dynamical behavior of TPP riboswitches: a comparison between Escherichia coli and Arabidopsis thaliana. PMID:30862893
Predicting protein-peptide interaction sites using distant protein complexes as structural templates. PMID:30862810
Vasodilation Elicited by Isoxsuprine, Identified by High-Throughput Virtual Screening of Compound Libraries, Involves Activation of the NO/cGMP and H₂S/KATP Pathways and Blockade of α₁-Adrenoceptors and Calcium Channels. PMID:30862086
Novel 8-Substituted Coumarins That Selectively Inhibit Human Carbonic Anhydrase IX and XII. PMID:30857344
Protein structure prediction. PMID:30853739
Dysregulation of TLR5 and TAM Ligands in the Alzheimer's Brain as Contributors to Disease Progression. PMID:30852796
Binding of Pb-Melatonin and Pb-(Melatonin-metabolites) complexes with DMT1 and ZIP8: implications for lead detoxification. PMID:30850959
Writing a wrong: Coupled RNA polymerase II transcription and RNA quality control. PMID:30848101
Molecular docking and dynamic studies of crepiside E beta glucopyranoside as an inhibitor of snake venom PLA2. PMID:30847632
Cross-Species Analysis of Glycosaminoglycan Binding Proteins Reveals Some Animal Models Are "More Equal" than Others. PMID:30845788
A stochastic simulation of skeletal muscle calcium transients in a structurally realistic sarcomere model using MCell. PMID:30845143
Identification of mNeonGreen as a pH-Dependent, Turn-On Fluorescent Protein Sensor for Chloride. PMID:30843313
Significantly different effects of tetrahydroberberrubine enantiomers on dopamine D1/D2 receptors revealed by experimental study and integrated in silico simulation. PMID:30840169
Autocrine motility factor promotes endometrial cancer progression by targeting GPER-1. PMID:30836961
Merits and pitfalls of conventional and covalent docking in identifying new hydroxyl aryl aldehyde like compounds as human IRE1 inhibitors. PMID:30833722
Hydrodynamic and Electrophoretic Properties of Trastuzumab/HER2 Extracellular Domain Complexes as Revealed by Experimental Techniques and Computational Simulations. PMID:30832287
RPITER: A Hierarchical Deep Learning Framework for ncRNA⁻Protein Interaction Prediction. PMID:30832218
Snails In Silico: A Review of Computational Studies on the Conopeptides. PMID:30832207
Stalis: A Computational Method for Template-Based Ab Initio Ligand Design. PMID:30829435
Hydrodynamic and Electrophoretic Properties of Trastuzumab/HER2 Extracellular Domain Complexes as Revealed by Experimental Techniques and Computational Simulations. PMID:30832287
RPITER: A Hierarchical Deep Learning Framework for ncRNA⁻Protein Interaction Prediction. PMID:30832218
Snails In Silico: A Review of Computational Studies on the Conopeptides. PMID:30832207
Stalis: A Computational Method for Template-Based Ab Initio Ligand Design. PMID:30829435
Extensive Reliability Evaluation of Docking-Based Target-Fishing Strategies. PMID:30818741
A network-centric approach to drugging TNF-induced NF-κB signaling. PMID:30808860
Metabolic gene NR4A1 as a potential therapeutic target for non-smoking female non-small cell lung cancer patients. PMID:30806032
PKAD: a database of experimentally measured pKa values of ionizable groups in proteins. PMID:30805645
Cholesterol bound Plasmodium falciparum co-chaperone 'PFA0660w' complexes with major virulence factor 'PfEMP1' via chaperone 'PfHsp70-x'. PMID:30804381
BRN2 suppresses apoptosis, reprograms DNA damage repair, and is associated with a high somatic mutation burden in melanoma. PMID:30804224
An alkaline active feruloyl-CoA synthetase from soil metagenome as a potential key enzyme for lignin valorization strategies. PMID:30802241
DAMpred: Recognizing Disease-Associated nsSNPs through Bayes-Guided Neural-Network Model Built on Low-Resolution Structure Prediction of Proteins and Protein-Protein Interactions. PMID:30796987
The inhibitory mechanism of aurintricarboxylic acid targeting serine/threonine phosphatase Stp1 in Staphylococcus aureus: insights from molecular dynamics simulations. PMID:30796354
Capture and display of antibodies secreted by hybridoma cells enables fluorescent on-cell screening. PMID:30794061
Phagocytosis of Aspergillus fumigatus by Human Bronchial Epithelial Cells Is Mediated by the Arp2/3 Complex and WIPF2. PMID:30792969
Molecular features of steroid-binding antidins and their use for assaying serum progesterone. PMID:30785944
Metal based donepezil analogues designed to inhibit human acetylcholinesterase for Alzheimer's disease. PMID:30785927
An Integrative Database of β-Lactamase Enzymes: Sequences, Structures, Functions, and Phylogenetic Trees. PMID:30783007
9-Methylfascaplysin Is a More Potent Aβ Aggregation Inhibitor than the Marine-Derived Alkaloid, Fascaplysin, and Produces Nanomolar Neuroprotective Effects in SH-SY5Y Cells. PMID:30781608
Shedding Light on the Interaction of Human Anti-Apoptotic Bcl-2 Protein with Ligands through Biophysical and in Silico Studies. PMID:30781512
Identifying individual risk rare variants using protein structure guided local tests (POINT). PMID:30779729
Discovery of Amantamide, a Selective CXCR7 Agonist from Marine Cyanobacteria. PMID:30779584
Circadian oscillator proteins across the kingdoms of life: structural aspects. PMID:30777051
A Long-Acting PYY3-36 Analog Mediates Robust Anorectic Efficacy with Minimal Emesis in Nonhuman Primates. PMID:30773465
Tertiary Structural Motif Sequence Statistics Enable Facile Prediction and Design of Peptides that Bind Anti-apoptotic Bfl-1 and Mcl-1. PMID:30773399
A multiepitopic theoretical fusion construct based on in-silico epitope screening of known vaccine candidates for protection against wide range of enterobacterial pathogens. PMID:30769032
In Silico Genome-Wide Analysis of the ATP-Binding Cassette Transporter Gene Family in Soybean (Glycine max L.) and Their Expression Profiling. PMID:30766888
Five computational developability guidelines for therapeutic antibody profiling. PMID:30765520
MultiDomainBenchmark: a multi-domain query and subject database suite. PMID:30764761
Characterization of Differential Dynamics, Specificity, and Allostery of Lipoxygenase Family Members. PMID:30762363
Machine Learning Identifies Chemical Characteristics That Promote Enzyme Catalysis. PMID:30761897
Web-based display of protein surface and pH-dependent properties for assessing the developability of biotherapeutics. PMID:30760735
Convergent perturbation of the human domain-resolved interactome by viruses and mutations inducing similar disease phenotypes. PMID:30759076
Selecting Near-Native Protein Structures from Predicted Decoy Sets Using Ordered Graphlet Degree Similarity. PMID:30754721
A combined computational strategy of sequence and structural analysis predicts the existence of a functional eicosanoid pathway in Drosophila melanogaster. PMID:30753230
Mechanism of hydrogen peroxide formation by lytic polysaccharide monooxygenase. PMID:30746099
De Novo Structural Pattern Mining in Cellular Electron Cryotomograms. PMID:30744995
Molecular interaction studies of Deguelin and its derivatives with Cyclin D1 and Cyclin E in cancer cell signaling pathway: The computational approach. PMID:30741976
Homology models of mouse and rat estrogen receptor-α ligand-binding domain created by in silico mutagenesis of a human template: molecular docking with 17ß-estradiol, diethylstilbestrol, and paraben analogs. PMID:30740556
rBAN: retro-biosynthetic analysis of nonribosomal peptides. PMID:30737579
Homogentisate 1,2-dioxygenase (HGD) gene variants, their analysis and genotype-phenotype correlations in the largest cohort of patients with AKU. PMID:30737480
Targeting Loxosceles spider Sphingomyelinase D with small-molecule inhibitors as a potential therapeutic approach for loxoscelism. PMID:30734604
Screening of anti-inflammatory phytocompounds from Crateva adansonii leaf extracts and its validation by in silico modeling. PMID:30733792
Tailoring the properties of (catalytically)-active inclusion bodies. PMID:30732596
Myxococcus xanthus truncated globin HbO: in silico analysis and functional characterization. PMID:30729391
Breaking tolerance with engineered class I antigen-presenting molecules. PMID:30728302
Structure-function characterization of an insecticidal protein GNIP1Aa, a member of an MACPF and β-tripod families. PMID:30728296
Aminoacyl tRNA synthetases as malarial drug targets: a comparative bioinformatics study. PMID:30728021
Autophagy and Apoptosis Specific Knowledgebases-guided Systems Pharmacology Drug Research. PMID:30727895
4-(3-Nitrophenyl)thiazol-2-ylhydrazone derivatives as antioxidants and selective hMAO-B inhibitors: synthesis, biological activity and computational analysis. PMID:30727777
ZincBind-the database of zinc binding sites. PMID:30722040
'Candidatus Ornithobacterium hominis': insights gained from draft genomes obtained from nasopharyngeal swabs. PMID:30720420
P-glycoprotein Inhibitor Tariquidar Potentiates Efficacy of Astragaloside IV in Experimental Autoimmune Encephalomyelitis Mice. PMID:30717494
DeepDrug3D: Classification of ligand-binding pockets in proteins with a convolutional neural network. PMID:30716081
Quantitative insights into the cyanobacterial cell economy. PMID:30714903
Functional Evolution of Proteins. PMID:30714210
A functional interplay between intein and extein sequences in protein splicing compensates for the essential block B histidine. PMID:30713635
Tetrazoles via Multicomponent Reactions. PMID:30707567
Computational Investigation on Electrostatic Loop Mutants Instigating Destabilization and Aggregation on Human SOD1 Protein Causing Amyotrophic Lateral Sclerosis. PMID:30701485
Inherent versus induced protein flexibility: Comparisons within and between apo and holo structures. PMID:30699115
Insight into novel RNA-binding activities via large-scale analysis of lncRNA-bound proteome and IDH1-bound transcriptome. PMID:30698743
Cys.sqlite: A Structured-Information Approach to the Comprehensive Analysis of Cysteine Disulfide Bonds in the Protein Databank. PMID:30694665
Computational Studies Applied to Flavonoids against Alzheimer's and Parkinson's Diseases. PMID:30693065
Novel Approach for the Search for Chemical Scaffolds with Dual Activity with Acetylcholinesterase and the α7 Nicotinic Acetylcholine Receptor-A Perspective for the Treatment of Neurodegenerative Disorders. PMID:30691196
ccPDB 2.0: an updated version of datasets created and compiled from Protein Data Bank. PMID:30689843
Predicting protein-ligand binding modes for CELPP and GC3: workflows and insight. PMID:30689079
Spectrum of neurodevelopmental disease associated with the GNAO1 guanosine triphosphate-binding region. PMID:30682224
Dissecting a novel allosteric mechanism of cruzain: A computer-aided approach. PMID:30682119
Enhancing Side Chain Rotamer Sampling Using Nonequilibrium Candidate Monte Carlo. PMID:30677291
The role of the tyrosine kinase Wzc (Sll0923) and the phosphatase Wzb (Slr0328) in the production of extracellular polymeric substances (EPS) by Synechocystis PCC 6803. PMID:30675753
How to design potent and selective DYRK1B inhibitors? Molecular modeling study. PMID:30673861
Structural consequence of the most frequently recurring cancer-associated substitution in DNA polymerase ε. PMID:30670696
Computational modeling of RNA 3D structure based on experimental data. PMID:30670629
Endoplasmic Reticulum Chaperone Glucose-Regulated Protein 94 Is Essential for Proinsulin Handling. PMID:30670477
Selective Targeting of the Interconversion between Glucosylceramide and Ceramide by Scaffold Tailoring of Iminosugar Inhibitors. PMID:30669468
Towards Unraveling the Histone Code by Fragment Blind Docking. PMID:30669446
PEPCONF, a diverse data set of peptide conformational energies. PMID:30667382
Digoxin, an Overlooked Agonist of RORγ/RORγT. PMID:30666196
Oxazole-Bridged Combretastatin A-4 Derivatives with Tethered Hydroxamic Acids: Structure⁻Activity Relations of New Inhibitors of HDAC and/or Tubulin Function. PMID:30658435
Synthesis, In Silico, and In Vitro Evaluation of Long Chain Alkyl Amides from 2-Amino-4-Quinolone Derivatives as Biofilm Inhibitors. PMID:30658415
Alsterpaullone induces apoptosis of HepG2 cells via a p38 mitogen-activated protein kinase signaling pathway. PMID:30655881
Organic cation transporter 3 (Oct3) is a distinct catecholamines clearance route in adipocytes mediating the beiging of white adipose tissue. PMID:30653498
PDB_Amyloid: an extended live amyloid structure list from the PDB. PMID:30652085
Recurrent activating mutations of PPARγ associated with luminal bladder tumors. PMID:30651555
A Computational Method to Propose Mutations in Enzymes Based on Structural Signature Variation (SSV). PMID:30650542
Interface residues of transient protein-protein complexes have extensive intra-protein interactions apart from inter-protein interactions. PMID:30646935
Synthesis and Biological Investigation of Phenothiazine-Based Benzhydroxamic Acids as Selective Histone Deacetylase 6 Inhibitors. PMID:30645113
How Effectively Can Adaptive Sampling Methods Capture Spontaneous Ligand Binding? PMID:30645108
Iron-sulfur clusters have no right angles. PMID:30644841
Functional annotation of orthologs in metagenomes: a case study of genes for the transformation of oceanic dimethylsulfoniopropionate. PMID:30643200
Resveratrol and Its Human Metabolites-Effects on Metabolic Health and Obesity. PMID:30641865
Translational control mechanisms in cutaneous malignant melanoma: the role of eIF2α. PMID:30634982
Enterococcus faecium TIR-Domain Genes Are Part of a Gene Cluster Which Promotes Bacterial Survival in Blood. PMID:30631364
The (R)-enantiomer of the 6-chromanol derivate SUL-121 improves renal graft perfusion via antagonism of the α1-adrenoceptor. PMID:30626882
Prediction of deleterious mutations in coding regions of mammals with transfer learning. PMID:30622632
Scalable Extraction of Big Macromolecular Data in Azure Data Lake Environment. PMID:30621295
Powdery Mildews Are Characterized by Contracted Carbohydrate Metabolism and Diverse Effectors to Adapt to Obligate Biotrophic Lifestyle. PMID:30619222
Diversity of opisthokont septin proteins reveals structural constraints and conserved motifs. PMID:30616529
Protein-protein binding supersites. PMID:30615604
CS-ROSETTA. PMID:30611429
CS-ROSETTA. PMID:30611429
Structure and function prediction of arsenate reductase from Deinococcus indicus DR1. PMID:30610463
Aflatoxin B₁⁻Formamidopyrimidine DNA Adducts: Relationships between Structures, Free Energies, and Melting Temperatures. PMID:30609733
Electrostatic explanation of D1228V/H/N-induced c-Met resistance and sensitivity to type I and type II kinase inhibitors in targeted gastric cancer therapy. PMID:30607513
Molecular docking and dynamics of Nickel-Schiff base complexes for inhibiting β-lactamase of Mycobacterium tuberculosis. PMID:30607319
Molecular docking and ADME properties of bioactive molecules against human acid-beta-glucosidase enzyme, cause of Gaucher's disease. PMID:30607316
In silico quest of selective naphthyl-based CREBBP bromodomain inhibitor. PMID:30607314
Grafting, Stripping and Stapling of Helical Peptides from the Dimerization Interface of ONFH-Related Bone Morphogenetic Protein-2. PMID:30604108
Alarmones as Vestiges of a Bygone RNA World. PMID:30604017
Characterization of novel lignocellulose-degrading enzymes from the porcupine microbiome using synthetic metagenomics. PMID:30601862
Numerical Encodings of Amino Acids in Multivariate Gaussian Modeling of Protein Multiple Sequence Alignments. PMID:30597916
How Structural Biologists and the Protein Data Bank Contributed to Recent FDA New Drug Approvals. PMID:30595456
Systematics for types and effects of DNA variations. PMID:30591019
Accurate calculation of side chain packing and free energy with applications to protein molecular dynamics. PMID:30589846
Structural Insights into Characterizing Binding Sites in Epidermal Growth Factor Receptor Kinase Mutants. PMID:30582689
Exploring protein-protein interactions using the site-identification by ligand competitive saturation methodology. PMID:30582220
In-silico Antigenicity Determination and Clustering of Dengue Virus Serotypes. PMID:30581453
Identifying Potential Ageing-Modulating Drugs In Silico. PMID:30581056
Clinically Relevant Post-Translational Modification Analyses-Maturing Workflows and Bioinformatics Tools. PMID:30577541
Foundry: a message-oriented, horizontally scalable ETL system for scientific data integration and enhancement. PMID:30576493
PhytoTypeDB: a database of plant protein inter-cultivar variability and function. PMID:30576486
The dilemma of bacterial expansins evolution. The unusual case of Streptomyces acidiscabies and Kutzneria sp. 744. PMID:30574264
The study of degradation mechanisms of glyco-engineered plant produced anti-rabies monoclonal antibodies E559 and 62-71-3. PMID:30571707
Adevonin, a novel synthetic antimicrobial peptide designed from the Adenanthera pavonina trypsin inhibitor (ApTI) sequence. PMID:30570384
RIP-MD: a tool to study residue interaction networks in protein molecular dynamics. PMID:30568854
A Novel Selective JAK2 Inhibitor Identified Using Pharmacological Interactions. PMID:30564118
Deciphering evolution of immune recognition in antibodies. PMID:30563492
Methods for Discovering and Targeting Druggable Protein-Protein Interfaces and Their Application to Repurposing. PMID:30547433
Activity Landscape and Molecular Modeling to Explore the SAR of Dual Epigenetic Inhibitors: A Focus on G9a and DNMT1. PMID:30544967
Structural characterization and molecular dynamics simulations of the caprine and bovine solute carrier family 11 A1 (SLC11A1). PMID:30543052
Chemoenzymatic synthesis of glycopeptides bearing rare N-glycan sequences with or without bisecting GlcNAc. PMID:30542567
Orphan Receptor GPR88 as an Emerging Neurotherapeutic Target. PMID:30540906
Implications of protein conformations to modifying novel inhibitor Oseltamivir for 2009 H1N1 influenza A virus by simulation and docking studies. PMID:30539048
A Small Cyclic β-Hairpin Peptide Mimics the Rbfox2 RNA Recognition Motif and Binds to the Precursor miRNA 20b. PMID:30537200
Partner-specific prediction of RNA-binding residues in proteins: A critical assessment. PMID:30536635
Systematic domain-based aggregation of protein structures highlights DNA-, RNA- and other ligand-binding positions. PMID:30535108
Molecular pathogenesis of human CD59 deficiency. PMID:30533526
PremPDI estimates and interprets the effects of missense mutations on protein-DNA interactions. PMID:30533007
PathFX provides mechanistic insights into drug efficacy and safety for regulatory review and therapeutic development. PMID:30532240
Outlier analyses of the Protein Data Bank archive using a probability-density-ranking approach. PMID:30532050
Inhibitor binding mode and allosteric regulation of Na+-glucose symporters. PMID:30532032
Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models. PMID:30531987
Structural and functional characterization of an intradiol ring-cleavage dioxygenase from the polyphagous spider mite herbivore Tetranychus urticae Koch. PMID:30529144
Deamidation and isomerization liability analysis of 131 clinical-stage antibodies. PMID:30526254
Chemical Composition and Antifungal In Vitro and In Silico, Antioxidant, and Anticholinesterase Activities of Extracts and Constituents of Ouratea fieldingiana (DC.) Baill. PMID:30524481
Gastroprotective effect of araloside A on ethanol- and aspirin-induced gastric ulcer in mice: involvement of H+/K+-ATPase and mitochondrial-mediated signaling pathway. PMID:30523551
Structural assembly of the megadalton-sized receptor for intestinal vitamin B12 uptake and kidney protein reabsorption. PMID:30523278
Rotational and translational positions determine the structural and dynamic impact of a single ribonucleotide incorporated in the nucleosome. PMID:30522887
Comparative analysis of interactions between aryl hydrocarbon receptor ligand binding domain with its ligands: a computational study. PMID:30522477
Antimicrobial peptide similarity and classification through rough set theory using physicochemical boundaries. PMID:30522443
Protein-protein interaction sites prediction by ensemble random forests with synthetic minority oversampling technique. PMID:30520961
Gene ontology improves template selection in comparative protein docking. PMID:30520123
DHS (trans-4,4'-dihydroxystilbene) suppresses DNA replication and tumor growth by inhibiting RRM2 (ribonucleotide reductase regulatory subunit M2). PMID:30518875
Genetic variations in human papillomavirus and cervical cancer outcomes. PMID:30515767
Structure-function analysis of Sedolisins: evolution of tripeptidyl peptidase and endopeptidase subfamilies in fungi. PMID:30514213
Reoptimized UNRES Potential for Protein Model Quality Assessment. PMID:30513992
Do environmentally induced DNA variations mediate adaptation in Aspergillus flavus exposed to chromium stress in tannery sludge? PMID:30509176
Design of a Novel and Selective IRAK4 Inhibitor Using Topological Water Network Analysis and Molecular Modeling Approaches. PMID:30501110
SCOPe: classification of large macromolecular structures in the structural classification of proteins-extended database. PMID:30500919
Distinguishing crystallographic from biological interfaces in protein complexes: role of intermolecular contacts and energetics for classification. PMID:30497368
canSAR: update to the cancer translational research and drug discovery knowledgebase. PMID:30496479
A robust method for the estimation and visualization of IgE cross-reactivity likelihood between allergens belonging to the same protein family. PMID:30496313
Coevolving residues inform protein dynamics profiles and disease susceptibility of nSNVs. PMID:30496278
Mapping the Proteome of the Synaptic Cleft through Proximity Labeling Reveals New Cleft Proteins. PMID:30487426
Downstream TRPM4 Polymorphisms Are Associated with Intracranial Hypertension and Statistically Interact with ABCC8 Polymorphisms in a Prospective Cohort of Severe Traumatic Brain Injury. PMID:30484364
Three-dimensional descriptors for aminergic GPCRs: dependence on docking conformation and crystal structure. PMID:30484023
Selective agonist of TRPML2 reveals direct role in chemokine release from innate immune cells. PMID:30479274
Deep scanning lysine metabolism in Escherichia coli. PMID:30478237
Butyrivibrio hungatei MB2003 Competes Effectively for Soluble Sugars Released by Butyrivibrio proteoclasticus B316T during Growth on Xylan or Pectin. PMID:30478228
Proteomics of nucleocytoplasmic partitioning. PMID:30472625
Structural Survey of Broadly Neutralizing Antibodies Targeting the HIV-1 Env Trimer Delineates Epitope Categories and Characteristics of Recognition. PMID:30471922
Presence of Intra-helical Salt-Bridge in Loop E Half-Helix Can Influence the Transport Properties of AQP1 and GlpF Channels: Molecular Dynamics Simulations of In Silico Mutants. PMID:30470864
A structural-chemical explanation of fungal laccase activity. PMID:30470810
Long-range molecular dynamics show that inactive forms of Protein Kinase A are more dynamic than active forms. PMID:30468265
On the Mechanism of Action of Anti-Inflammatory Activity of Hypericin: An In Silico Study Pointing to the Relevance of Janus Kinases Inhibition. PMID:30467287
A close look onto structural models and primary ligands of metallo-β-lactamases. PMID:30466711
Label-Free Electrophoretic Mobility Shift Assay (EMSA) for Measuring Dissociation Constants of Protein-RNA Complexes. PMID:30461222
Toward development of generic inhibitors against the 3C proteases of picornaviruses. PMID:30461192
Trapping and Driving Individual Charged Micro-particles in Fluid with an Electrostatic Device. PMID:30460287
The ubiquitin ligase SspH1 from Salmonella uses a modular and dynamic E3 domain to catalyze substrate ubiquitylation. PMID:30459234
Peptide-based PET quantifies target engagement of PD-L1 therapeutics. PMID:30457978
qFit-ligand Reveals Widespread Conformational Heterogeneity of Drug-Like Molecules in X-Ray Electron Density Maps. PMID:30457858
Pharmacoinformatic Approach to Explore the Antidote Potential of Phytochemicals on Bungarotoxin from Indian Krait, Bungarus caeruleus. PMID:30455855
Combining bioinformatics, cheminformatics, functional genomics and whole organism approaches for identifying epigenetic drug targets in Schistosoma mansoni. PMID:30455056
A Multi-model Approach to Assessing Local and Global Cryo-EM Map Quality. PMID:30449687
PAVOOC: designing CRISPR sgRNAs using 3D protein structures and functional domain annotations. PMID:30445568
The SUPERFAMILY 2.0 database: a significant proteome update and a new webserver. PMID:30445555
Probing inhibition mechanisms of adenosine deaminase by using molecular dynamics simulations. PMID:30444912
Structural disorder in the proteome and interactome of Alkhurma virus (ALKV). PMID:30443749
A guide to maximizing the therapeutic potential of protein-polymer conjugates by rational design. PMID:30443654
Chemoinformatics Strategies for Leishmaniasis Drug Discovery. PMID:30443215
Large-Scale Analyses of Site-Specific Evolutionary Rates across Eukaryote Proteomes Reveal Confounding Interactions between Intrinsic Disorder, Secondary Structure, and Functional Domains. PMID:30441862
Learning structural motif representations for efficient protein structure search. PMID:30423083
The MemProtMD database: a resource for membrane-embedded protein structures and their lipid interactions. PMID:30418645
Homology modeling and in vivo functional characterization of the zinc permeation pathway in a heavy metal P-type ATPase. PMID:30418580
Improved Modeling of Halogenated Ligand-Protein Interactions Using the Drude Polarizable and CHARMM Additive Empirical Force Fields. PMID:30418023
Refining the macromolecular model - achieving the best agreement with the data from X-ray diffraction experiment. PMID:30416256
Discovery of three RNA viruses using ant transcriptomic datasets. PMID:30415391
Binding Analysis of the Inositol-Requiring Enzyme 1 Kinase Domain. PMID:30411035
Folding of Gα Subunits: Implications for Disease States. PMID:30411001
A benchmark driven guide to binding site comparison: An exhaustive evaluation using tailor-made data sets (ProSPECCTs). PMID:30408032
Cancer3D 2.0: interactive analysis of 3D patterns of cancer mutations in cancer subsets. PMID:30407596
Proteomic Profiling of Burkholderia thailandensis During Host Infection Using Bio-Orthogonal Noncanonical Amino Acid Tagging (BONCAT). PMID:30406044
In silico Prediction, Characterization, Molecular Docking, and Dynamic Studies on Fungal SDRs as Novel Targets for Searching Potential Fungicides Against Fusarium Wilt in Tomato. PMID:30405403
Antagonists for Constitutively Active Mutant Estrogen Receptors: Insights into the Roles of Antiestrogen-Core and Side-Chain. PMID:30404440
ezCADD: A Rapid 2D/3D Visualization-Enabled Web Modeling Environment for Democratizing Computer-Aided Drug Design. PMID:30403855
Insight into novel clinical mutants of RpsA-S324F, E325K, and G341R of Mycobacterium tuberculosis associated with pyrazinamide resistance. PMID:30402208
In Silico Study Reveals How E64 Approaches, Binds to, and Inhibits Falcipain-2 of Plasmodium falciparum that Causes Malaria in Humans. PMID:30401806
Predicting CD4 T-cell epitopes based on antigen cleavage, MHCII presentation, and TCR recognition. PMID:30399156
A bacterial immunomodulatory protein with lipocalin-like domains facilitates host-bacteria mutualism in larval zebrafish. PMID:30398151
A dual-functional priming-capping loop of rhabdoviral RNA polymerases directs terminal de novo initiation and capping intermediate formation. PMID:30395342
Flexibility and structure of flanking DNA impact transcription factor affinity for its core motif. PMID:30395339
PlantPAN3.0: a new and updated resource for reconstructing transcriptional regulatory networks from ChIP-seq experiments in plants. PMID:30395277
MemBrain: An Easy-to-Use Online Webserver for Transmembrane Protein Structure Prediction. PMID:30393651
GPCR homology model template selection benchmarking: Global versus local similarity measures. PMID:30390544
A Perspective on Thiazolidinone Scaffold Development as a New Therapeutic Strategy for Toxoplasmosis. PMID:30386743
Design of metalloproteins and novel protein folds using variational autoencoders. PMID:30385875
Exploring the PXR ligand binding mechanism with advanced Molecular Dynamics methods. PMID:30385820
Deciphering the structure of the condensin protein complex. PMID:30385633
Revealing Unknown Protein Structures Using Computational Conformational Sampling Guided by Experimental Hydrogen-Exchange Data. PMID:30384411
A planarian nidovirus expands the limits of RNA genome size. PMID:30383829
"Infostery" analysis of short molecular dynamics simulations identifies highly sensitive residues and predicts deleterious mutations. PMID:30382169
A fully automatic method yielding initial models from high-resolution cryo-electron microscopy maps. PMID:30377346
Using a Consensus Docking Approach to Predict Adverse Drug Reactions in Combination Drug Therapies for Gulf War Illness. PMID:30373189
Refinement of protein-protein complexes in contact map space with metadynamics simulations. PMID:30370948
MDockPeP: An ab-initio protein-peptide docking server. PMID:30368849
Quantum chemical and molecular mechanics studies on the assessment of interactions between resveratrol and mutant SOD1 (G93A) protein. PMID:30368622
AlloMAPS: allosteric mutation analysis and polymorphism of signaling database. PMID:30365033
Characterization of Monoclonal Antibody-Protein Antigen Complexes Using Small-Angle Scattering and Molecular Modeling. PMID:30364605
Comparison of Quantitative and Qualitative (Q)SAR Models Created for the Prediction of Ki and IC50 Values of Antitarget Inhibitors. PMID:30364128
From cycloheptathiophene-3-carboxamide to oxazinone-based derivatives as allosteric HIV-1 ribonuclease H inhibitors. PMID:30362381
Could the presence of sodium ion influence the accuracy and precision of the ligand-posing in the human A2A adenosine receptor orthosteric binding site using a molecular docking approach? Insights from Dockbench. PMID:30361971
CRISPR-Cas9 human gene replacement and phenomic characterization in Caenorhabditis elegans to understand the functional conservation of human genes and decipher variants of uncertain significance. PMID:30361258
Differential orientation and conformation of surface-bound keratinocyte growth factor on (hydroxyethyl)methacrylate, (hydroxyethyl)methacrylate/methyl methacrylate, and (hydroxyethyl)methacrylate/methacrylic acid hydrogel copolymers. PMID:30360629
In Silico Studies on Compounds Derived from Calceolaria: Phenylethanoid Glycosides as Potential Multitarget Inhibitors for the Development of Pesticides. PMID:30360548
RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy. PMID:30357411
EncoMPASS: an online database for analyzing structure and symmetry in membrane proteins. PMID:30357403
Protein Data Bank: the single global archive for 3D macromolecular structure data. PMID:30357364
Small-molecule CaVα1⋅CaVβ antagonist suppresses neuronal voltage-gated calcium-channel trafficking. PMID:30355767
A combined computational and experimental approach reveals the structure of a C/EBPβ-Spi1 interaction required for IL1B gene transcription. PMID:30355733
Design and Synthesis of Potent HIV-1 Protease Inhibitors Containing Bicyclic Oxazolidinone Scaffold as the P2 Ligands: Structure-Activity Studies and Biological and X-ray Structural Studies. PMID:30354121
Characterization and improved properties of Glutamine synthetase from Providencia vermicola by site-directed mutagenesis. PMID:30353099
Discovery and Structure-Activity-Relationship Study of N-Alkyl-5-hydroxypyrimidinone Carboxamides as Novel Antitubercular Agents Targeting Decaprenylphosphoryl-β-d-ribose 2'-Oxidase. PMID:30350998
Designed Functional Dispersion for Insulin Protection from Pepsin Degradation and Skeletal Muscle Cell Proliferation: In Silico and In Vitro Study. PMID:30347680
Fullerene Derivatives of Nucleoside HIV Reverse Transcriptase Inhibitors-In Silico Activity Prediction. PMID:30347655
Genetic diversity in two Plasmodium vivax protein ligands for reticulocyte invasion. PMID:30346980
Molecular docking studies of human MCT8 protein with soy isoflavones in Allan-Herndon-Dudley syndrome (AHDS). PMID:30345146
Carnosol suppresses patient-derived gastric tumor growth by targeting RSK2. PMID:30344937
Analysis of drug resistance in HIV protease. PMID:30343664
CRISPRO: identification of functional protein coding sequences based on genome editing dense mutagenesis. PMID:30340514
Design, synthesis, and X-ray studies of potent HIV-1 protease inhibitors incorporating aminothiochromane and aminotetrahydronaphthalene carboxamide derivatives as the P2 ligands. PMID:30340140
POPPeT: a New Method to Predict the Protection Factor of Backbone Amide Hydrogens. PMID:30338451
The Pioglitazone Trek via Human PPAR Gamma: From Discovery to a Medicine at the FDA and Beyond. PMID:30337873
Understanding molecular consequences of putative drug resistant mutations in Mycobacterium tuberculosis. PMID:30337649
Machine learning and structural analysis of Mycobacterium tuberculosis pan-genome identifies genetic signatures of antibiotic resistance. PMID:30333483
Resveratrol: Twenty Years of Growth, Development and Controversy. PMID:30332889
Pharmacophore modeling, docking and molecular dynamics to identify Leishmania major farnesyl pyrophosphate synthase inhibitors. PMID:30327889
Exploring Configuration Space and Path Space of Biomolecules Using Enhanced Sampling Techniques-Searching for Mechanism and Kinetics of Biomolecular Functions. PMID:30326661
Analysis of impact metrics for the Protein Data Bank. PMID:30325351
Application of molecular dynamics simulations to design a dual-purpose oligopeptide linker sequence for fusion proteins. PMID:30324504
Comparison of Peptide Ion Conformers Arising from Non-Helical and Helical Peptides Using Ion Mobility Spectrometry and Gas-Phase Hydrogen/Deuterium Exchange. PMID:30324261
KinaMetrix: a web resource to investigate kinase conformations and inhibitor space. PMID:30321373
Large-scale docking predicts that sORF-encoded peptides may function through protein-peptide interactions in Arabidopsis thaliana. PMID:30321192
Conformational Sampling of Macrocyclic Drugs in Different Environments: Can We Find the Relevant Conformations? PMID:30320271
Empirical Scoring Functions for Structure-Based Virtual Screening: Applications, Critical Aspects, and Challenges. PMID:30319422
Crystal structure of the major quadruplex formed in the promoter region of the human c-MYC oncogene. PMID:30312328
Distinctive structural motifs co-ordinate the catalytic nucleophile and the residues of the oxyanion hole in the alpha/beta-hydrolase fold enzymes. PMID:30311984
An open-source software ecosystem for the interactive exploration of ultrafast electron scattering data. PMID:30310764
Prediction of disulfide dihedral angles using chemical shifts. PMID:30310586
Crystallography and Its Impact on Carbonic Anhydrase Research. PMID:30302289
Decision-Tree Based Meta-Strategy Improved Accuracy of Disorder Prediction and Identified Novel Disordered Residues Inside Binding Motifs. PMID:30301243
Mining the cellular inventory of pyridoxal phosphate-dependent enzymes with functionalized cofactor mimics. PMID:30297752
Pattern to Knowledge: Deep Knowledge-Directed Machine Learning for Residue-Residue Interaction Prediction. PMID:30287904
Two Engineered OBPs with opposite temperature-dependent affinities towards 1-aminoanthracene. PMID:30287882
Why are Hoogsteen base pairs energetically disfavored in A-RNA compared to B-DNA? PMID:30285154
Molecular modeling investigation of the potential mechanism for phytochemical-induced skin collagen biosynthesis by inhibition of the protein phosphatase 1 holoenzyme. PMID:30284191
Structural basis of inactivation of Ras and Rap1 small GTPases by Ras/Rap1-specific endopeptidase from the sepsis-causing pathogen Vibrio vulnificus. PMID:30282804
Protein refractive index increment is determined by conformation as well as composition. PMID:30280702
Interactions of cantharidin-like inhibitors with human protein phosphatase-5 in a Mg2+ system: molecular dynamics and quantum calculations. PMID:30280322
Using bioinformatics tools for the discovery of Dengue RNA-dependent RNA polymerase inhibitors. PMID:30280009
Computational analysis of the amino acid interactions that promote or decrease protein solubility. PMID:30279585
Impact of Genomics on Clarifying the Evolutionary Relationships amongst Mycobacteria: Identification of Molecular Signatures Specific for the Tuberculosis-Complex of Bacteria with Potential Applications for Novel Diagnostics and Therapeutics. PMID:30279355
Reversible and Tunable Photoswitching of Protein Function through Genetic Encoding of Azobenzene Amino Acids in Mammalian Cells. PMID:30277634
Contribution of an unusual CDR2 element of a single domain antibody in ricin toxin binding affinity and neutralizing activity. PMID:30265352
Strengths and Weaknesses of Molecular Simulations of Electrosprayed Droplets. PMID:30259408
Filamentous Aggregates of Tau Proteins Fulfil Standard Amyloid Criteria Provided by the Fuzzy Oil Drop (FOD) Model. PMID:30257460
Enhanced activity of Withania somnifera family-1 glycosyltransferase (UGT73A16) via mutagenesis. PMID:30255239
Heterogeneous Solvation in Distinctive Protein-Protein Interfaces Revealed by Molecular Dynamics Simulations. PMID:30252476
Structural Identification and Systematic Comparison of Phorbol Ester, Dioleoylglycerol, Alcohol and Sevoflurane Binding Sites in PKCδ C1A Domain. PMID:30251087
The functional diversity of Aurora kinases: a comprehensive review. PMID:30250494
Deep generative models of genetic variation capture the effects of mutations. PMID:30250057
Adnectin-drug conjugates for Glypican-3-specific delivery of a cytotoxic payload to tumors. PMID:30247737
Temperature-Induced Replacement of Phosphate Proton with Metal Ion Captured in Neutron Structures of A-DNA. PMID:30244969
Tick galactosyltransferases are involved in α-Gal synthesis and play a role during Anaplasma phagocytophilum infection and Ixodes scapularis tick vector development. PMID:30242261
Oxidative Alteration of Trp-214 and Lys-199 in Human Serum Albumin Increases Binding Affinity with Phenylbutazone: A Combined Experimental and Computational Investigation. PMID:30241420
Template-Guided Protein Structure Prediction and Refinement Using Optimized Folding Landscape Force Fields. PMID:30240202
THE-DB: a threading model database for comparative protein structure analysis of the E. coli K12 and human proteomes. PMID:30239678
Potential Deoxycytidine Kinase Inhibitory Activity of Amaryllidaceae Alkaloids: An In Silico Approach. PMID:30237684
Proteinase 3; a potential target in chronic obstructive pulmonary disease and other chronic inflammatory diseases. PMID:30236095
Exploring the Structural Mechanism of Covalently Bound E3 Ubiquitin Ligase: Catalytic or Allosteric Inhibition? PMID:30232697
Deep Sequencing of H7N9 Influenza A Viruses from 16 Infected Patients from 2013 to 2015 in Shanghai Reveals Genetic Diversity and Antigenic Drift. PMID:30232169
Evolution of gene knockout strains of E. coli reveal regulatory architectures governed by metabolism. PMID:30228271
All-atom normal mode dynamics of HIV-1 capsid. PMID:30226840
Au courant computation of the PDB to audit diffraction anisotropy of soluble and membrane proteins. PMID:30225276
Receptor pharmacophore ensemble (REPHARMBLE): a probabilistic pharmacophore modeling approach using multiple protein-ligand complexes. PMID:30220049
Accurate flexible refinement of atomic models against medium-resolution cryo-EM maps using damped dynamics. PMID:30219048
Calculate protein-ligand binding affinities with the extended linear interaction energy method: application on the Cathepsin S set in the D3R Grand Challenge 3. PMID:30218199
Electrostatic mechanism of V600E mutation-induced B-Raf constitutive activation in colorectal cancer: molecular implications for the selectivity difference between type-I and type-II inhibitors. PMID:30218115
Exploring the Ligand Efficacy of Cannabinoid Receptor 1 (CB1) using Molecular Dynamics Simulations. PMID:30213978
Structural insights into antigen recognition of an anti-β-(1,6)-β-(1,3)-D-glucan antibody. PMID:30209318
DaReUS-Loop: accurate loop modeling using fragments from remote or unrelated proteins. PMID:30209260
Searching for 3D structural models from a library of biological shapes using a few 2D experimental images. PMID:30208849
Blinded evaluation of cathepsin S inhibitors from the D3RGC3 dataset using molecular docking and free energy calculations. PMID:30206740
Understanding the role of glucose regulated protein 170 (GRP170) as a nucleotide exchange factor through molecular simulations. PMID:30205291
Nature-inspired engineering of an F-type lectin for increased binding strength. PMID:30202877
Analyzing protein topology based on Laguerre tessellation of a pore-traversing water network. PMID:30202114
CpAMs induce assembly of HBV capsids with altered electrophoresis mobility: Implications for mechanism of inhibiting pgRNA packaging. PMID:30201396
Structure of the Fc fragment of the NIST reference antibody RM8671. PMID:30198883
Bend-Induced Twist Waves and the Structure of Nucleosomal DNA. PMID:30192578
Targeting Metalloenzymes for Therapeutic Intervention. PMID:30192523
Identification of a perchloric acid-soluble protein (PSP)-like ribonuclease from Trichomonas vaginalis. PMID:30191309
Online structure-based screening of purchasable approved drugs and natural compounds: retrospective examples of drug repositioning on cancer targets. PMID:30190791
An integrated strategy for identifying new targets and inferring the mechanism of action: taking rhein as an example. PMID:30189851
Bridging Molecular Docking to Molecular Dynamics in Exploring Ligand-Protein Recognition Process: An Overview. PMID:30186166
The porcine odorant-binding protein as molecular probe for benzene detection. PMID:30183769
Five Years of the KNIME Vernalis Cheminformatics Community Contribution. PMID:30182834
Encoding canonical DNA quadruplex structure. PMID:30182059
Effects of Acetylation and Phosphorylation on Subunit Interactions in Three Large Eukaryotic Complexes. PMID:30181345
Tinker 8: Software Tools for Molecular Design. PMID:30176213
Stress-induced nuclear depletion of Entamoeba histolytica 3'-5' exoribonuclease EhRrp6 and its role in growth and erythrophagocytosis. PMID:30171071
Extra precision glide docking, free energy calculation and molecular dynamics studies of 1,2-diarylethane derivatives as potent urease inhibitors. PMID:30159776
Grxcr2 is required for stereocilia morphogenesis in the cochlea. PMID:30157177
Correlation of phenotype with genotype and protein structure in RYR1-related disorders. PMID:30155738
Who's on base? Revealing the catalytic mechanism of inverting family 6 glycoside hydrolases. PMID:30155195
Human T cell receptor occurrence patterns encode immune history, genetic background, and receptor specificity. PMID:30152754
Role of solvent accessibility for aggregation-prone patches in protein folding. PMID:30150761
Membrane Active Peptides and Their Biophysical Characterization. PMID:30135402
IDP⁻CRF: Intrinsically Disordered Protein/Region Identification Based on Conditional Random Fields. PMID:30135358
bioSyntax: syntax highlighting for computational biology. PMID:30134911
Complete genome of streamlined marine actinobacterium Pontimonas salivibrio strain CL-TW6T adapted to coastal planktonic lifestyle. PMID:30134835
Protein-ligand binding enthalpies from near-millisecond simulations: Analysis of a preorganization paradox. PMID:30134726
Catalytic Mechanism of Amyloid-β Peptide Degradation by Insulin Degrading Enzyme: Insights from Quantum Mechanics and Molecular Mechanics Style Møller-Plesset Second Order Perturbation Theory Calculation. PMID:30133282
Analysis of C3 Gene Variants in Patients With Idiopathic Recurrent Spontaneous Pregnancy Loss. PMID:30131807
Protein-ligand pose and affinity prediction: Lessons from D3R Grand Challenge 3. PMID:30128928
Crystal Structures of R-Type Bacteriocin Sheath and Tube Proteins CD1363 and CD1364 From Clostridium difficile in the Pre-assembled State. PMID:30127773
PPInS: a repository of protein-protein interaction sitesbase. PMID:30127348
Multifunctional Proteins: Involvement in Human Diseases and Targets of Current Drugs. PMID:30123928
Protein Motion and Configurations in a Form-Fitting Nanopore: Avidin in ClyA. PMID:30122294
Microenvironmental control of glucose metabolism in tumors by regulation of pyruvate dehydrogenase. PMID:30121950
Mathematical deep learning for pose and binding affinity prediction and ranking in D3R Grand Challenges. PMID:30116918
In silico identification of inhibitors against Plasmodium falciparum histone deacetylase 1 (PfHDAC-1). PMID:30109440
Interaction of indomethacin with calf thymus DNA: a multi-spectroscopic, thermodynamic and molecular modelling approach. PMID:30108839
Development of NMR and thermal shift assays for the evaluation of Mycobacterium tuberculosis isocitrate lyase inhibitors. PMID:30108733
Structure modeling to function prediction of Uncharacterized Human Protein C15orf41. PMID:30108417
A molecular simulation analysis of vitamin D targets interleukin 13 (IL13) as an alternative to mometasone in asthma. PMID:30105198
DNArCdb: A database of cancer biomarkers in DNA repair genes that includes variants related to multiple cancer phenotypes. PMID:30098577
The Recognition of Unrelated Ligands by Identical Proteins. PMID:30095890
afpCOOL: A tool for antifreeze protein prediction. PMID:30094375
Protein-RNA interactions: structural characteristics and hotspot amino acids. PMID:30093489
Computational design of new protein kinase 2 inhibitors for the treatment of inflammatory diseases using QSAR, pharmacophore-structure-based virtual screening, and molecular dynamics. PMID:30088101
Conformational transition pathway of R308K mutant glucokinase in the presence of the glucokinase activator YNKGKA4. PMID:30087826
Oligomerization of bacterially expressed H1N1 recombinant hemagglutinin contributes to protection against viral challenge. PMID:30087372
Recent applications of deep learning and machine intelligence on in silico drug discovery: methods, tools and databases. PMID:30084866
Shape similarity guided pose prediction: lessons from D3R Grand Challenge 3. PMID:30084081
Structurally Mapping Antibody Repertoires. PMID:30083160
Truly Target-Focused Pharmacophore Modeling: A Novel Tool for Mapping Intermolecular Surfaces. PMID:30082611
How does binding of agonist ligands control intrinsic molecular dynamics in human NMDA receptors? PMID:30075003
Genome-Wide Identification and Characterization of NODULE-INCEPTION-Like Protein (NLP) Family Genes in Brassica napus. PMID:30072649
Characterization of the APETALA2/Ethylene-responsive factor (AP2/ERF) transcription factor family in sunflower. PMID:30068961
Identification of a novel c-Myc inhibitor with antitumor effects on multiple myeloma cells. PMID:30068698
Structural and Evolutionary Insights within the Polysaccharide Deacetylase Gene Family of Bacillus anthracis and Bacillus cereus. PMID:30065210
Map segmentation, automated model-building and their application to the Cryo-EM Model Challenge. PMID:30063987
Understanding the Positional Binding and Substrate Interaction of a Highly Thermostable GH10 Xylanase from Thermotoga maritima by Molecular Docking. PMID:30061529
LASSBio-1586, an N-acylhydrazone derivative, attenuates nociceptive behavior and the inflammatory response in mice. PMID:30059558
Differing epidemiological dynamics of Chikungunya virus in the Americas during the 2014-2015 epidemic. PMID:30059496
Ferulic Acid Rescues LPS-Induced Neurotoxicity via Modulation of the TLR4 Receptor in the Mouse Hippocampus. PMID:30058023
Interspecies Anticancer and Antimicrobial Activities of Genus Solanum and Estimation of Rutin by Validated UPLC-PDA Method. PMID:30057644
Comment on structural basis of DUX4/IGH-driven transactivation. PMID:30054554
Multiple Optimal Phenotypes Overcome Redox and Glycolytic Intermediate Metabolite Imbalances in Escherichia coli pgi Knockout Evolutions. PMID:30054360
Analysis of nanobody paratopes reveals greater diversity than classical antibodies. PMID:30053276
dbCAN-seq: a database of carbohydrate-active enzyme (CAZyme) sequence and annotation. PMID:30053267
Updates to the RNA mapping database (RMDB), version 2. PMID:30053264
eModel-BDB: a database of comparative structure models of drug-target interactions from the Binding Database. PMID:30052959
Glyco-engineered cell line and computational docking studies reveals enterotoxigenic Escherichia coli CFA/I fimbriae bind to Lewis a glycans. PMID:30050155
A model for hydrophobic protrusions on peripheral membrane proteins. PMID:30048443
In silico mutational analysis and identification of stability centers in human interleukin-4. PMID:30046620
The Impairment of TorsinA's Binding to and Interactions With Its Activator: An Atomistic Molecular Dynamics Study of Primary Dystonia. PMID:30042949
The Helicobacter pylori cell shape promoting protein Csd5 interacts with the cell wall, MurF, and the bacterial cytoskeleton. PMID:30039535
Molecular docking and pharmacological/toxicological assessment of a new compound designed from celecoxib and paracetamol by molecular hybridization. PMID:30039481
Allostery and cooperativity in multimeric proteins: bond-to-bond propensities in ATCase. PMID:30038211
Oleanolic Acids Inhibit Vascular Endothelial Growth Factor Receptor 2 Signaling in Endothelial Cells: Implication for Anti-Angiogenic Therapy. PMID:30037214
An Immunopharmacoinformatics Approach in Development of Vaccine and Drug Candidates for West Nile Virus. PMID:30035107
Structural Analysis of Phosphoserine Aminotransferase (Isoform 1) From Arabidopsis thaliana- the Enzyme Involved in the Phosphorylated Pathway of Serine Biosynthesis. PMID:30034403
Pseudomonas aeruginosa pyoverdine maturation enzyme PvdP has a noncanonical domain architecture and affords insight into a new subclass of tyrosinases. PMID:30030378
In silico prediction of novel residues involved in amyloid primary nucleation of human I56T and D67H lysozyme. PMID:30029603
The HIV-1 Reverse Transcriptase A62V Mutation Influences Replication Fidelity and Viral Fitness in the Context of Multi-Drug-Resistant Mutations. PMID:30029500
Discovery of Retinoic Acid-Related Orphan Receptor γt Inverse Agonists via Docking and Negative Image-Based Screening. PMID:30023945
X-ray-Structure-Based Identification of Compounds with Activity against Targets from Different Families and Generation of Templates for Multitarget Ligand Design. PMID:30023769
Predicting Binding Affinities for GPCR Ligands Using Free-Energy Perturbation. PMID:30023478
Conformational dynamics and enzyme evolution. PMID:30021929
SKEMPI 2.0: an updated benchmark of changes in protein-protein binding energy, kinetics and thermodynamics upon mutation. PMID:30020414
A coarse-grained approach to studying the interactions of the antimicrobial peptides aurein 1.2 and maculatin 1.1 with POPG/POPE lipid mixtures. PMID:30019106
Selenazolyl-hydrazones as Novel Selective MAO Inhibitors With Antiproliferative and Antioxidant Activities: Experimental and In-silico Studies. PMID:30018949
An integrative, multi-omics approach towards the prioritization of Klebsiella pneumoniae drug targets. PMID:30018343
Evaluation system and web infrastructure for the second cryo-EM model challenge. PMID:30017700
Automatic recognition of ligands in electron density by machine learning. PMID:30016407
Genome-wide association and HLA fine-mapping studies identify risk loci and genetic pathways underlying allergic rhinitis. PMID:30013184
Increasing the length of poly-pyrimidine bulges broadens RNA conformational ensembles with minimal impact on stacking energetics. PMID:30012568
Inter-subunit interactions drive divergent dynamics in mammalian and Plasmodium actin filaments. PMID:30011270
Antenna effect and phosphorescence spectra to find the location of drug tetracycline in bovine β-lactoglobulin A. PMID:30006868
Inhibition of protein interactions: co-crystalized protein-protein interfaces are nearly as good as holo proteins in rigid-body ligand docking. PMID:30003468
An account of solvent accessibility in protein-RNA recognition. PMID:30002431
Quinazolinone-Amino Acid Hybrids as Dual Inhibitors of EGFR Kinase and Tubulin Polymerization. PMID:30002297
Probing Substituents in the 1- and 3-Position: Tetrahydropyrazino-Annelated Water-Soluble Xanthine Derivatives as Multi-Target Drugs With Potent Adenosine Receptor Antagonistic Activity. PMID:29998095
Molecular dynamics-derived rotamer libraries for d-amino acids within homochiral and heterochiral polypeptides. PMID:29992252
Water Pharmacophore: Designing Ligands using Molecular Dynamics Simulations with Water. PMID:29991756
LMap: Shape-Preserving Local Mappings for Biomedical Visualization. PMID:29990124
New Deep Learning Methods for Protein Loop Modeling. PMID:29990046
Computational Design of Antiangiogenic Peptibody by Fusing Human IgG1 Fc Fragment and HRH Peptide: Structural Modeling, Energetic Analysis, and Dynamics Simulation of Its Binding Potency to VEGF Receptor. PMID:29989101
A Sequential Segment Based Alpha-Helical Transmembrane Protein Alignment Method. PMID:29989071
Annonacin promotes selective cancer cell death via NKA-dependent and SERCA-dependent pathways. PMID:29988040
From Virtual Reality to Immersive Analytics in Bioinformatics. PMID:29982237
Demystifying the pH dependent conformational changes of human heparanase pertaining to structure-function relationships: an in silico approach. PMID:29980923
Harmine, a dual-specificity tyrosine phosphorylation-regulated kinase (DYRK) inhibitor induces caspase-mediated apoptosis in neuroblastoma. PMID:29977157
SAFlex: A structural alphabet extension to integrate protein structural flexibility and missing data information. PMID:29975698
Identification of Antifungal Targets Based on Computer Modeling. PMID:29973534
Conformational Sampling of Small Molecules With iCon: Performance Assessment in Comparison With OMEGA. PMID:29971231
Dynamics and Thermodynamics of Transthyretin Association from Molecular Dynamics Simulations. PMID:29967786
An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12. PMID:29967418
In Silico Approaches Applied to the Study of Peptide Analogs of Ile-Pro-Ile in Relation to Their Dipeptidyl Peptidase IV Inhibitory Properties. PMID:29963014
The olive constituent oleuropein, as a PPARα agonist, markedly reduces serum triglycerides. PMID:29960113
Stochastic simulations of nanoparticle internalization through transferrin receptor dependent clathrin-mediated endocytosis. PMID:29959983
Expansion and diversification of the gibberellin receptor GIBBERELLIN INSENSITIVE DWARF1 (GID1) family in land plants. PMID:29956113
In Silico Screening of Isocitrate Lyase for Novel Anti-Buruli Ulcer Natural Products Originating from Africa. PMID:29954088
Methyl-CpG-binding (SmMBD2/3) and chromobox (SmCBX) proteins are required for neoblast proliferation and oviposition in the parasitic blood fluke Schistosoma mansoni. PMID:29953544
G protein-coupled receptors: the evolution of structural insight. PMID:29951585
mGPfusion: predicting protein stability changes with Gaussian process kernel learning and data fusion. PMID:29949987
Synthesis, docking and anticancer activity of azo-linked hybrids of 1,3,4-thia-/oxadiazoles with cyclic imides. PMID:29948580
Identification and Phenotypic Characterization of ZEBRA LEAF16 Encoding a β-Hydroxyacyl-ACP Dehydratase in Rice. PMID:29946330
Computational quantum chemistry, molecular docking, and ADMET predictions of imidazole alkaloids of Pilocarpus microphyllus with schistosomicidal properties. PMID:29944674
Trichomonas vaginalis metalloproteinase TvMP50 is a monomeric Aminopeptidase P-like enzyme. PMID:29936696
The A-Z of Zika drug discovery. PMID:29935345
Whole-genome sequencing reveals a recurrent missense mutation in the Connexin 46 (GJA3) gene causing autosomal-dominant lamellar cataract. PMID:29934635
A Data Driven Model for Predicting RNA-Protein Interactions based on Gradient Boosting Machine. PMID:29934510
New Chromane-Based Derivatives as Inhibitors of Mycobacterium tuberculosis Salicylate Synthase (MbtI): Preliminary Biological Evaluation and Molecular Modeling Studies. PMID:29933627
In Silico Structural Evaluation of Short Cationic Antimicrobial Peptides. PMID:29933540
A protein chimera strategy supports production of a model "difficult-to-express" recombinant target. PMID:29933498
Recent examples of α-ketoglutarate-dependent mononuclear non-haem iron enzymes in natural product biosyntheses. PMID:29932179
Exploring the functional impact of alternative splicing on human protein isoforms using available annotation sources. PMID:29931155
A selective method for optimizing ensemble docking-based experiments on an InhA Fully-Flexible receptor model. PMID:29929475
MinOmics, an Integrative and Immersive Tool for Multi-Omics Analysis. PMID:29927748
Improving small molecule virtual screening strategies for the next generation of therapeutics. PMID:29920436
Sustainable data and metadata management at the BD2K-LINCS Data Coordination and Integration Center. PMID:29917015
The dynamic and stress-adaptive signaling hub of 14-3-3: emerging mechanisms of regulation and context-dependent protein-protein interactions. PMID:29915393
Modulating D-amino acid oxidase (DAAO) substrate specificity through facilitated solvent access. PMID:29906280
5-Formylcytosine mediated DNA-protein cross-links block DNA replication and induce mutations in human cells. PMID:29905846
LeptoDB: an integrated database of genomics and proteomics resource of Leptospira. PMID:29905762
Introduction of novel thermostable α-amylases from genus Anoxybacillus and proposing to group the Bacillaceae related α-amylases under five individual GH13 subfamilies. PMID:29904894
Interactive Molecular Graphics for Augmented Reality Using HoloLens. PMID:29897886
Computational Modeling of Hepatitis C Virus Envelope Glycoprotein Structure and Recognition. PMID:29892287
An interactome perturbation framework prioritizes damaging missense mutations for developmental disorders. PMID:29892012
Amino Acid Chiral Selection Via Weak Interactions in Stellar Environments: Implications for the Origin of Life. PMID:29891867
Design, Synthesis, Cytotoxic Evaluation and Molecular Docking of New Fluoroquinazolinones as Potent Anticancer Agents with Dual EGFR Kinase and Tubulin Polymerization Inhibitory Effects. PMID:29891789
Biophysical Examination of the Calcium-Modulated Nickel-Binding Properties of Human Calprotectin Reveals Conformational Change in the EF-Hand Domains and His3Asp Site. PMID:29890074
Genotype-phenotype correlations of low-frequency variants in the complement system in renal disease and age-related macular degeneration. PMID:29888403
Cascade Ligand- and Structure-Based Virtual Screening to Identify New Trypanocidal Compounds Inhibiting Putrescine Uptake. PMID:29888213
A Computational Approach for Prioritizing Selection of Therapies Targeting Drug Resistant Variation in Anaplastic Lymphoma Kinase. PMID:29888064
Mesoscopic Rigid Body Modelling of the Extracellular Matrix Self-Assembly. PMID:29886454
Discovery and Biochemical Characterization of PlyP56, PlyN74, and PlyTB40-Bacillus Specific Endolysins. PMID:29883383
Recovering Actives in Multi-Antitarget and Target Design of Analogs of the Myosin II Inhibitor Blebbistatin. PMID:29881723
Predicting 3D structure and stability of RNA pseudoknots in monovalent and divalent ion solutions. PMID:29879103
An expanded allosteric network in PTP1B by multitemperature crystallography, fragment screening, and covalent tethering. PMID:29877794
Crystal structures of the PH domains from Lbc family of RhoGEFs bound to activated RhoA GTPase. PMID:29876405
Machine Learning Methods for X-Ray Scattering Data Analysis from Biomacromolecular Solutions. PMID:29874600
Putative role of invariant water molecules in the X-ray structures of family G fungal endoxylanases. PMID:29872022
Modeling transcriptional activation changes to Gal4 variants via structure-based computational mutagenesis. PMID:29868268
Chloroplastic Serine Hydroxymethyltransferase From Medicago truncatula: A Structural Characterization. PMID:29868052
Structural Changes Due to Antagonist Binding in Ligand Binding Pocket of Androgen Receptor Elucidated Through Molecular Dynamics Simulations. PMID:29867496
Validating Molecular Dynamics Simulations against Experimental Observables in Light of Underlying Conformational Ensembles. PMID:29864281
Investigation of protein quaternary structure via stoichiometry and symmetry information. PMID:29864163
Integration of in vitro and in silico perspectives to explain chemical characterization, biological potential and anticancer effects of Hypericum salsugineum: A pharmacologically active source for functional drug formulations. PMID:29864137
Redefining the Protein Kinase Conformational Space with Machine Learning. PMID:29861272
IUPred2A: context-dependent prediction of protein disorder as a function of redox state and protein binding. PMID:29860432
Sequence-based prediction of physicochemical interactions at protein functional sites using a function-and-interaction-annotated domain profile database. PMID:29859055
A Deep Learning Framework for Robust and Accurate Prediction of ncRNA-Protein Interactions Using Evolutionary Information. PMID:29858068
Computational Insight into the Effect of Natural Compounds on the Destabilization of Preformed Amyloid-β(1⁻40) Fibrils. PMID:29857500
Making data matter: Voxel printing for the digital fabrication of data across scales and domains. PMID:29854949
Carnosic Acid, a Natural Diterpene, Attenuates Arsenic-Induced Hepatotoxicity via Reducing Oxidative Stress, MAPK Activation, and Apoptotic Cell Death Pathway. PMID:29854073
Riboflavin Riboswitch Regulation: Hands-On Learning about the Role of RNA Structures in the Control of Gene Expression in Bacteria. PMID:29854064
NGL viewer: web-based molecular graphics for large complexes. PMID:29850778
HSYMDOCK: a docking web server for predicting the structure of protein homo-oligomers with Cn or Dn symmetry. PMID:29846641
Exploring the Dual Inhibitory Activity of Novel Anthranilic Acid Derivatives towards α-Glucosidase and Glycogen Phosphorylase Antidiabetic Targets: Design, In Vitro Enzyme Assay, and Docking Studies. PMID:29844263
How electrostatic networks modulate specificity and stability of collagen. PMID:29844169
SuperDCA for genome-wide epistasis analysis. PMID:29813016
Computational-based structural, functional and phylogenetic analysis of Enterobacter phytases. PMID:29805952
Self-Consistent Framework Connecting Experimental Proxies of Protein Dynamics with Configurational Entropy. PMID:29799751
HotSpot Wizard 3.0: web server for automated design of mutations and smart libraries based on sequence input information. PMID:29796670
Molecular Characterization and Directed Evolution of a Metagenome-Derived l-Cysteine Sulfinate Decarboxylase. PMID:29796005
Computer-aided design of amino acid-based therapeutics: a review. PMID:29795978
Kinact: a computational approach for predicting activating missense mutations in protein kinases. PMID:29788456
Open Conformation of the Escherichia coli Periplasmic Murein Tripeptide Binding Protein, MppA, at High Resolution. PMID:29783769
Insight into small molecule binding to the neonatal Fc receptor by X-ray crystallography and 100 kHz magic-angle-spinning NMR. PMID:29782488
A new insight into identification of in silico analysis of natural compounds targeting GPR120. PMID:29780684
Protein surface functionalisation as a general strategy for facilitating biomimetic mineralisation of ZIF-8. PMID:29780551
PKS-NRPS Enzymology and Structural Biology: Considerations in Protein Production. PMID:29779664
Design, Synthesis, and Biological Evaluation of Benzimidazole-Derived Biocompatible Copper(II) and Zinc(II) Complexes as Anticancer Chemotherapeutics. PMID:29772746
Assigning crystallographic electron densities with free energy calculations-The case of the fluoride channel Fluc. PMID:29771936
Functional insights from proteome-wide structural modeling of Treponema pallidum subspecies pallidum, the causative agent of syphilis. PMID:29769048
Design and Synthesis of Highly Potent HIV-1 Protease Inhibitors Containing Tricyclic Fused Ring Systems as Novel P2 Ligands: Structure-Activity Studies, Biological and X-ray Structural Analysis. PMID:29763303
A Multi-Omics Database for Parasitic Nematodes and Trematodes. PMID:29761465
PAGE4 and Conformational Switching: Insights from Molecular Dynamics Simulations and Implications for Prostate Cancer. PMID:29758263
Structural biology data archiving - where we are and what lies ahead. PMID:29749603
Structural Transition and Antibody Binding of EBOV GP and ZIKV E Proteins from Pre-Fusion to Fusion-Initiation State. PMID:29748487
Fingerprint-Based Machine Learning Approach to Identify Potent and Selective 5-HT2BR Ligands. PMID:29748476
TRAF1 Is Critical for Regulating the BRAF/MEK/ERK Pathway in Non-Small Cell Lung Carcinogenesis. PMID:29748372
HPEPDOCK: a web server for blind peptide-protein docking based on a hierarchical algorithm. PMID:29746661
CNNH_PSS: protein 8-class secondary structure prediction by convolutional neural network with highway. PMID:29745837
RaptorX-Angle: real-value prediction of protein backbone dihedral angles through a hybrid method of clustering and deep learning. PMID:29745828
ProteomeVis: a web app for exploration of protein properties from structure to sequence evolution across organisms' proteomes. PMID:29741573
Ensemble allosteric model: energetic frustration within the intrinsically disordered glucocorticoid receptor. PMID:29735729
Molecular structures of cdc2-like kinases in complex with a new inhibitor chemotype. PMID:29723265
Applying graph theory to protein structures: an Atlas of coiled coils. PMID:29722888
Molecular Characterization of Respiratory Syncytial Virus in Children With Repeated Infections With Subgroup B in the Philippines. PMID:29722817
Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation. PMID:29722803
Cation-π interactions in protein-ligand binding: theory and data-mining reveal different roles for lysine and arginine. PMID:29719674
Structure and hydrodynamics of a DNA G-quadruplex with a cytosine bulge. PMID:29718405
Influence of Na+ and Mg2+ ions on RNA structures studied with molecular dynamics simulations. PMID:29718375
Efficient flexible backbone protein-protein docking for challenging targets. PMID:29718115
Microfocus diffraction from different regions of a protein crystal: structural variations and unit-cell polymorphism. PMID:29717712
Exploring intrinsically disordered proteins in Chlamydomonas reinhardtii. PMID:29717210
Computational Characterization of Small Molecules Binding to the Human XPF Active Site and Virtual Screening to Identify Potential New DNA Repair Inhibitors Targeting the ERCC1-XPF Endonuclease. PMID:29710850
Structural and functional dissection of differentially expressed tomato WRKY transcripts in host defense response against the vascular wilt pathogen (Fusarium oxysporum f. sp. lycopersici). PMID:29709017
Automated evaluation of quaternary structures from protein crystals. PMID:29708963
Evidence That Speciation of Oxovanadium Complexes Does Not Solely Account for Inhibition of Leishmania Acid Phosphatases. PMID:29707535
Positive and Negative Regulation of Angiogenesis by Soluble Vascular Endothelial Growth Factor Receptor-1. PMID:29702562
Comparative systems analysis of the secretome of the opportunistic pathogen Aspergillus fumigatus and other Aspergillus species. PMID:29700415
PDZscape: a comprehensive PDZ-protein database. PMID:29699484
Targeting AKT with Oridonin Inhibits Growth of Esophageal Squamous Cell Carcinoma In Vitro and Patient-Derived Xenografts In Vivo. PMID:29695636
Oligomeric interfaces as a tool in drug discovery: Specific interference with activity of malate dehydrogenase of Plasmodium falciparum in vitro. PMID:29694407
Identification of errors in the IEDB using ontologies. PMID:29688357
Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data. PMID:29688351
Computational Protein Design with Deep Learning Neural Networks. PMID:29679026
Structure refinement of membrane proteins via molecular dynamics simulations. PMID:29675899
A Novel Method for Drug Screen to Regulate G Protein-Coupled Receptors in the Metabolic Network of Alzheimer's Disease. PMID:29675426
Characterizing metal-binding sites in proteins with X-ray crystallography. PMID:29674755
Lactoferrin is a natural inhibitor of plasminogen activation. PMID:29669808
BEST1 protein stability and degradation pathways differ between autosomal dominant Best disease and autosomal recessive bestrophinopathy accounting for the distinct retinal phenotypes. PMID:29668979
Molecular evolution and functional divergence of alcohol dehydrogenases in animals, fungi and plants. PMID:29668010
Prediction of GPCR-Ligand Binding Using Machine Learning Algorithms. PMID:29666662
Integrating Cross-Linking Experiments with Ab Initio Protein-Protein Docking. PMID:29665372
Structural studies on radiopharmaceutical DOTA-minigastrin analogue (CP04) complexes and their interaction with CCK2 receptor. PMID:29663167
PKIDB: A Curated, Annotated and Updated Database of Protein Kinase Inhibitors in Clinical Trials. PMID:29662024
Backbone Brackets and Arginine Tweezers delineate Class I and Class II aminoacyl tRNA synthetases. PMID:29659563
Identification of avian vasotocin receptor subtype-specific antagonists involved in the stress response of the chicken, Gallus gallus. PMID:29658387
Development of a Prototype System for Archiving Integrative/Hybrid Structure Models of Biological Macromolecules. PMID:29657133
The Relation between α-Helical Conformation and Amyloidogenicity. PMID:29653837
Novel Insights for Inhibiting Mutant Heterodimer IDH1wt-R132H in Cancer: An In-Silico Approach. PMID:29651790
Identification by Molecular Docking ofHomoisoflavones from Leopoldia comosa as Ligands of Estrogen Receptors. PMID:29649162
Zidovudine ameliorates pathology in the mouse model of Duchenne muscular dystrophy via P2RX7 purinoceptor antagonism. PMID:29642926
Holistic Approach to Partial Covalent Interactions in Protein Structure Prediction and Design with Rosetta. PMID:29641200
O-GlcNAcase Fragment Discovery with Fluorescence Polarimetry. PMID:29641181
How Diverse Are the Protein-Bound Conformations of Small-Molecule Drugs and Cofactors? PMID:29637066
Fisetin Confers Cardioprotection against Myocardial Ischemia Reperfusion Injury by Suppressing Mitochondrial Oxidative Stress and Mitochondrial Dysfunction and Inhibiting Glycogen Synthase Kinase 3β Activity. PMID:29636855
Exploration of the effect of sequence variations located inside the binding pocket of HIV-1 and HIV-2 proteases. PMID:29636521
A low-barrier hydrogen bond mediates antibiotic resistance in a noncanonical catalytic triad. PMID:29632894
Improving Docking Performance Using Negative Image-Based Rescoring. PMID:29632488
Synergistic effects of H3 and H4 nucleosome tails on structure and dynamics of a lesion-containing DNA: Binding of a displaced lesion partner base to the H3 tail for GG-NER recognition. PMID:29631253
Activity of bromodomain protein inhibitors/binders against asexual-stage Plasmodium falciparum parasites. PMID:29631126
Crystal Structures of Cystathionine β-Synthase from Saccharomyces cerevisiae: One Enzymatic Step at a Time. PMID:29630349
Structural analyses of Arabidopsis thaliana legumain γ reveal differential recognition and processing of proteolysis and ligation substrates. PMID:29628443
Multiple spectral channels in branchiopods. I. Vision in dim light and neural correlates. PMID:29622664
In silico characterization of a cyanobacterial plant-type isoaspartyl aminopeptidase/asparaginase. PMID:29619654
Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas. PMID:29617664
Virtual screening, Docking, ADMET and System Pharmacology studies on Garcinia caged Xanthone derivatives for Anticancer activity. PMID:29615704
Protein-bound NAD(P)H Lifetime is Sensitive to Multiple Fates of Glucose Carbon. PMID:29615678
Advances in HIV-1 Vaccine Development. PMID:29614779
FoldX accurate structural protein-DNA binding prediction using PADA1 (Protein Assisted DNA Assembly 1). PMID:29608705
Modeling Structure and Dynamics of Protein Complexes with SAXS Profiles. PMID:29605933
Evolution of photosynthetic reaction centers: insights from the structure of the heliobacterial reaction center. PMID:29603081
Accurately Predicting Disordered Regions of Proteins Using Rosetta ResidueDisorder Application. PMID:29595057
HERV Envelope Proteins: Physiological Role and Pathogenic Potential in Cancer and Autoimmunity. PMID:29593697
A Novel Dual HDAC6 and Tubulin Inhibitor, MPT0B451, Displays Anti-tumor Ability in Human Cancer Cells in Vitro and in Vivo. PMID:29593536
Active site remodeling during the catalytic cycle in metal-dependent fructose-1,6-bisphosphate aldolases. PMID:29593097
The complete mitochondrial genome of the hermaphroditic freshwater mussel Anodonta cygnea (Bivalvia: Unionidae): in silico analyses of sex-specific ORFs across order Unionoida. PMID:29587633
Water-mediated conformational preselection mechanism in substrate binding cooperativity to protein kinase A. PMID:29581285
Exploring the structural origins of cryptic sites on proteins. PMID:29581267
Gene expression profiles of ion channels and receptors in mouse resistance arteries: Effects of cell type, vascular bed, and age. PMID:29577514
Docking-based inverse virtual screening: methods, applications, and challenges. PMID:29577065
ProtaBank: A repository for protein design and engineering data. PMID:29575358
Systematic characterization of pan-cancer mutation clusters. PMID:29572294
Comparative analysis of nanobody sequence and structure data. PMID:29569425
Lipophosphoglycan 3 From Leishmania infantum chagasi Binds Heparin With Micromolar Affinity. PMID:29568220
Novel Semisynthetic Derivatives of Bile Acids as Effective Tyrosyl-DNA Phosphodiesterase 1 Inhibitors. PMID:29562592
Evaluation of variability in high-resolution protein structures by global distance scoring. PMID:29560428
The Ever-Evolving Concept of the Gene: The Use of RNA/Protein Experimental Techniques to Understand Genome Functions. PMID:29560353
Identification of new inhibitors against human Great wall kinase using in silico approaches. PMID:29559668
ADPredict: ADP-ribosylation site prediction based on physicochemical and structural descriptors. PMID:29554239
Structure of the Mitochondrial Aminolevulinic Acid Synthase, a Key Heme Biosynthetic Enzyme. PMID:29551290
A novel interaction fingerprint derived from per atom score contributions: exhaustive evaluation of interaction fingerprint performance in docking based virtual screening. PMID:29549526
Scalable total synthesis and comprehensive structure-activity relationship studies of the phytotoxin coronatine. PMID:29549326
Serial Femtosecond Crystallography of G Protein-Coupled Receptors. PMID:29543504
Prediction and interpretation of deleterious coding variants in terms of protein structural stability. PMID:29540703
Packing Density of the Amyloid Precursor Protein in the Cell Membrane. PMID:29539399
De novo discovery of structural motifs in RNA 3D structures through clustering. PMID:29534235
Molecular Cloning and Characterization of Carbonic Anhydrase XII from Pufferfish (Takifugu rubripes). PMID:29534037
Distributed computing for macromolecular crystallography. PMID:29533240
A molecular dynamics approach to explore the structural characterization of cataract causing mutation R58H on human γD crystallin. PMID:29532225
Proteome-wide mapping of immune features onto Plasmodium protein three-dimensional structures. PMID:29531293
Revising the Structural Diversity of Ribosomal Proteins Across the Three Domains of Life. PMID:29529322
An unexpected vestigial protein complex reveals the evolutionary origins of an s-triazine catabolic enzyme. PMID:29523689
Network Analysis of Protein Adaptation: Modeling the Functional Impact of Multiple Mutations. PMID:29522102
Synthesis, Molecular Docking, and Antimycotic Evaluation of Some 3-Acyl Imidazo[1,2-a]pyrimidines. PMID:29518930
Prediction of sensitivity to gefitinib/erlotinib for EGFR mutations in NSCLC based on structural interaction fingerprints and multilinear principal component analysis. PMID:29514601
Cysteine peptidases of Eudiplozoon nipponicum: a broad repertoire of structurally assorted cathepsins L in contrast to the scarcity of cathepsins B in an invasive species of haematophagous monogenean of common carp. PMID:29510760
Building protein-protein interaction networks for Leishmania species through protein structural information. PMID:29510668
Immunodominance in T cell responses elicited against different domains of detoxified pneumolysin PlyD1. PMID:29509778
Determination of an effective scoring function for RNA-RNA interactions with a physics-based double-iterative method. PMID:29506237
RPiRLS: Quantitative Predictions of RNA Interacting with Any Protein of Known Sequence. PMID:29495575
Ligand-induced perturbation of the HIF-2α:ARNT dimer dynamics. PMID:29489822
Discovery of Molidustat (BAY 85-3934): A Small-Molecule Oral HIF-Prolyl Hydroxylase (HIF-PH) Inhibitor for the Treatment of Renal Anemia. PMID:29485740
Screening, large-scale production and structure-based classification of cystine-dense peptides. PMID:29483648
How large B-factors can be in protein crystal structures. PMID:29471780
Tracking the route of molecular oxygen in O2-tolerant membrane-bound [NiFe] hydrogenase. PMID:29463722
Identification of Novel Protein Kinase Receptor Type 2 Inhibitors Using Pharmacophore and Structure-Based Virtual Screening. PMID:29463017
A Novel Interaction Between the TLR7 and a Colchicine Derivative Revealed Through a Computational and Experimental Study. PMID:29462934
Mechanistic insights into transferable polymyxin resistance among gut bacteria. PMID:29462787
Synthesis of Highly Substituted Imidazole Uracil Containing Molecules via Ugi-4CR and Passerini-3CR. PMID:29457887
A Novel Approach to Data Collection for Difficult Structures: Data Management for Large Numbers of Crystals with the BLEND Software. PMID:29456874
Molecular Simulation Studies of 3,3'-Diindolylmethane as a Potent MicroRNA-21 Antagonist. PMID:29456377
Comprehensive Analysis of Constraint on the Spatial Distribution of Missense Variants in Human Protein Structures. PMID:29455857
StructureMapper: a high-throughput algorithm for analyzing protein sequence locations in structural data. PMID:29452363
An in silico argument for mitochondrial microRNA as a determinant of primary non function in liver transplantation. PMID:29449571
Ligand-mediated protein degradation reveals functional conservation among sequence variants of the CUL4-type E3 ligase substrate receptor cereblon. PMID:29449372
Competition between abiogenic Al3+ and native Mg2+, Fe2+ and Zn2+ ions in protein binding sites: implications for aluminum toxicity. PMID:29445953
Identification of Bichalcones as Sirtuin Inhibitors by Virtual Screening and In Vitro Testing. PMID:29443909
RNA Dependent RNA Polymerases: Insights from Structure, Function and Evolution. PMID:29439438
AMOEBA Polarizable Atomic Multipole Force Field for Nucleic Acids. PMID:29438622
Design of Highly Potent, Dual-Acting and Central-Nervous-System-Penetrating HIV-1 Protease Inhibitors with Excellent Potency against Multidrug-Resistant HIV-1 Variants. PMID:29437300
The unique fold and lability of the [2Fe-2S] clusters of NEET proteins mediate their key functions in health and disease. PMID:29435647
Dynamics of the Interaction of RecG Protein with Stalled Replication Forks. PMID:29432678
WDL-RF: predicting bioactivities of ligand molecules acting with G protein-coupled receptors by combining weighted deep learning and random forest. PMID:29432522
Improving succinylation prediction accuracy by incorporating the secondary structure via helix, strand and coil, and evolutionary information from profile bigrams. PMID:29432431
Design of peptide-based epitope vaccine and further binding site scrutiny led to groundswell in drug discovery against Lassa virus. PMID:29430345
Molecular structure and catalytic mechanism of fungal family G acidophilic xylanases. PMID:29430342
New Insights into the Function and Global Distribution of Polyethylene Terephthalate (PET)-Degrading Bacteria and Enzymes in Marine and Terrestrial Metagenomes. PMID:29427431
Pi-Pi contacts are an overlooked protein feature relevant to phase separation. PMID:29424691
CoeViz: A Web-Based Integrative Platform for Interactive Visualization of Large Similarity and Distance Matrices. PMID:29423399
Embelin Restores Carbapenem Efficacy against NDM-1-Positive Pathogens. PMID:29422890
Easy and fast method for expression and native extraction of Plasmodium vivax Duffy binding protein fragments. PMID:29422046
Structural prediction of protein models using distance restraints derived from cross-linking mass spectrometry data. PMID:29419816
Decoys Selection in Benchmarking Datasets: Overview and Perspectives. PMID:29416509
Peptide Level Turnover Measurements Enable the Study of Proteoform Dynamics. PMID:29414762
Involvement of PKA/DARPP-32/PP1α and β- arrestin/Akt/GSK-3β Signaling in Cadmium-Induced DA-D2 Receptor-Mediated Motor Dysfunctions: Protective Role of Quercetin. PMID:29410441
Plasticizers used in food-contact materials affect adipogenesis in 3T3-L1 cells. PMID:29410257
Systematic prediction of DNA shape changes due to CpG methylation explains epigenetic effects on protein-DNA binding. PMID:29409522
The Affinity of Brominated Phenolic Compounds for Human and Zebrafish Thyroid Receptor β: Influence of Chemical Structure. PMID:29409039
Computational Assessment of Pharmacokinetics and Biological Effects of Some Anabolic and Androgen Steroids. PMID:29404794
Effects of urea, metal ions and surfactants on the binding of baicalein with bovine serum albumin. PMID:29403991
Using RNA Sequence and Structure for the Prediction of Riboswitch Aptamer: A Comprehensive Review of Available Software and Tools. PMID:29403526
Water-mediated correlations in DNA-enzyme interactions. PMID:29403145
A computationally driven analysis of the polyphenol-protein interactome. PMID:29396566
Carbamates as Potential Prodrugs and a New Warhead for HDAC Inhibition. PMID:29393896
Pre-clinical effects of metformin and aspirin on the cell lines of different breast cancer subtypes. PMID:29392539
EzMol: A Web Server Wizard for the Rapid Visualization and Image Production of Protein and Nucleic Acid Structures. PMID:29391170
Experimental maps of DNA structure at nucleotide resolution distinguish intrinsic from protein-induced DNA deformations. PMID:29390080
Characterization of homodimer interfaces with cross-linking mass spectrometry and isotopically labeled proteins. PMID:29388937
The Design and Development of Potent Small Molecules as Anticancer Agents Targeting EGFR TK and Tubulin Polymerization. PMID:29385728
G2S: a web-service for annotating genomic variants on 3D protein structures. PMID:29385402
Enabling the hypothesis-driven prioritization of ligand candidates in big databases: Screenlamp and its application to GPCR inhibitor discovery for invasive species control. PMID:29383467
Large scale analysis of protein conformational transitions from aqueous to non-aqueous media. PMID:29382320
KLF1 gene and borderline hemoglobin A2 in Saudi population. PMID:29379553
High-resolution structure prediction of β-barrel membrane proteins. PMID:29378944
A statistical model for improved membrane protein expression using sequence-derived features. PMID:29378850
Identification of the Autochaperone Domain in the Type Va Secretion System (T5aSS): Prevalent Feature of Autotransporters with a β-Helical Passenger. PMID:29375499
Identification of a Golgi GPI-N-acetylgalactosamine transferase with tandem transmembrane regions in the catalytic domain. PMID:29374258
Screening a small molecule library to identify inhibitors of NF-κB inducing kinase and pro-labor genes in human placenta. PMID:29374256
Automated NMR resonance assignments and structure determination using a minimal set of 4D spectra. PMID:29374165
Anti-ROR1 scFv-EndoG as a Novel Anti-Cancer Therapeutic Drug. PMID:29373898
Microtubule-Actin Crosslinking Factor 1 and Plakins as Therapeutic Drug Targets. PMID:29373494
Quasiharmonic Analysis of the Energy Landscapes of Dihydrofolate Reductase from Piezophiles and Mesophiles. PMID:29370701
A systematic analysis of nucleosome core particle and nucleosome-nucleosome stacking structure. PMID:29367745
Cardiolipin dynamics and binding to conserved residues in the mitochondrial ADP/ATP carrier. PMID:29366674
Informing Efforts to Develop Nitroreductase for Amine Production. PMID:29364838
Success: evolutionary and structural properties of amino acids prove effective for succinylation site prediction. PMID:29363424
Mapping HLA-A2, -A3 and -B7 supertype-restricted T-cell epitopes in the ebolavirus proteome. PMID:29363421
Toxicodynamics of Mycotoxins in the Framework of Food Risk Assessment-An In Silico Perspective. PMID:29360783
Gene annotation bias impedes biomedical research. PMID:29358745
nextPARS: parallel probing of RNA structures in Illumina. PMID:29358234
Inhibitors of Trypanosoma cruzi Sir2 related protein 1 as potential drugs against Chagas disease. PMID:29357372
Structural Characterization and Function Prediction of Immunoglobulin-like Fold in Cell Adhesion and Cell Signaling. PMID:29356528
Interactome INSIDER: a structural interactome browser for genomic studies. PMID:29355848
Evaluating hydrophobic galactonoamidines as transition state analogs for enzymatic β-galactoside hydrolysis. PMID:29353731
An "All-In-One" Pharmacophoric Architecture for the Discovery of Potential Broad-Spectrum Anti-Flavivirus Drugs. PMID:29349531
CRISPR RNA and anti-CRISPR protein binding to the Xanthomonas albilineans Csy1-Csy2 heterodimer in the type I-F CRISPR-Cas system. PMID:29348170
DataMed - an open source discovery index for finding biomedical datasets. PMID:29346583
Identification of novel leishmanicidal molecules by virtual and biochemical screenings targeting Leishmania eukaryotic translation initiation factor 4A. PMID:29346371
KIX domain of AtMed15a, a Mediator subunit of Arabidopsis, is required for its interaction with different proteins. PMID:29341856
3D-e-Chem: Structural Cheminformatics Workflows for Computer-Aided Drug Discovery. PMID:29337438
Disruptor of telomeric silencing 1-like (DOT1L): disclosing a new class of non-nucleoside inhibitors by means of ligand-based and structure-based approaches. PMID:29335872
Validation of tautomeric and protomeric binding modes by free energy calculations. A case study for the structure based optimization of D-amino acid oxidase inhibitors. PMID:29335871
Modeling the assembly order of multimeric heteroprotein complexes. PMID:29329283
The role of IL‑16 gene polymorphisms in endometriosis. PMID:29328375
Interaction of anthraquinones of Cassia occidentalis seeds with DNA and Glutathione. PMID:29326881
Investigation into Improving the Aqueous Solubility of the Thieno[2,3-b]pyridine Anti-Proliferative Agents. PMID:29324695
Advantages of a distant cellulase catalytic base. PMID:29321205
Pharmacophore Modeling and in Silico/in Vitro Screening for Human Cytochrome P450 11B1 and Cytochrome P450 11B2 Inhibitors. PMID:29312923
Affinity maturation of a portable Fab-RNA module for chaperone-assisted RNA crystallography. PMID:29309709
Representability of algebraic topology for biomolecules in machine learning based scoring and virtual screening. PMID:29309403
A systematic analysis of atomic protein-ligand interactions in the PDB. PMID:29308120
Computational Modeling of the Staphylococcal Enterotoxins and Their Interaction with Natural Antitoxin Compounds. PMID:29301344
fDETECT webserver: fast predictor of propensity for protein production, purification, and crystallization. PMID:29295714
Aqueous ionic liquids influence the disulfide bond isoform equilibrium in conotoxin AuIB: a consequence of the Hofmeister effect? PMID:29294259
Coordinated regulation of intracellular pH by two glucose-sensing pathways in yeast. PMID:29284676
Nanoparticle size and production efficiency are affected by the presence of fatty acids during albumin nanoparticle fabrication. PMID:29281685
High-resolution global peptide-protein docking using fragments-based PIPER-FlexPepDock. PMID:29281622
Design, Synthesis and Cytotoxic Evaluation of Novel Chalcone Derivatives Bearing Triazolo[4,3-a]-quinoxaline Moieties as Potent Anticancer Agents with Dual EGFR Kinase and Tubulin Polymerization Inhibitory Effects. PMID:29280968
Structural Dynamics Control Allosteric Activation of Cytohesin Family Arf GTPase Exchange Factors. PMID:29276036
2-Methoxyestradiol Affects Mitochondrial Biogenesis Pathway and Succinate Dehydrogenase Complex Flavoprotein Subunit A in Osteosarcoma Cancer Cells. PMID:29275365
CSmetaPred: a consensus method for prediction of catalytic residues. PMID:29273005
Evaluation of β-Amino Acid Replacements in Protein Loops: Effects on Conformational Stability and Structure. PMID:29272560
Computational Studies of Snake Venom Toxins. PMID:29271884
Small molecule purine and pseudopurine derivatives: synthesis, cytostatic evaluations and investigation of growth inhibitory effect in non-small cell lung cancer A549. PMID:29271659
The crystal structure of Z-DNA with untypically coordinated Ca2+ ions. PMID:29270817
Conformational Ensembles of α-Synuclein Derived Peptide with Different Osmolytes from Temperature Replica Exchange Sampling. PMID:29270108
Atomistic simulations and network-based modeling of the Hsp90-Cdc37 chaperone binding with Cdk4 client protein: A mechanism of chaperoning kinase clients by exploiting weak spots of intrinsically dynamic kinase domains. PMID:29267381
Molecular Dynamics Simulations Reveal an Interplay between SHAPE Reagent Binding and RNA Flexibility. PMID:29265824
"Inverse Drug Discovery" Strategy To Identify Proteins That Are Targeted by Latent Electrophiles As Exemplified by Aryl Fluorosulfates. PMID:29265822
Behavior of BsoBI endonuclease in the presence and absence of DNA. PMID:29264670
Nuclear Localization of Apolipoprotein E4: A New Trick for an Old Protein. PMID:29264400
What contributes to an effective mannose recognition domain? PMID:29259668
Allosteric modulation of protein-protein interactions by individual lipid binding events. PMID:29259178
Peptide Uptake Is Essential for Borrelia burgdorferi Viability and Involves Structural and Regulatory Complexity of its Oligopeptide Transporter. PMID:29259089
GPCR Modulation of Thieno[2,3-b]pyridine Anti-Proliferative Agents. PMID:29258235
Utilizing knowledge base of amino acids structural neighborhoods to predict protein-protein interaction sites. PMID:29244012
Mitochondrial complex III Rieske Fe-S protein processing and assembly. PMID:29243944
A novel missense mutation in HSF4 causes autosomal-dominant congenital lamellar cataract in a British family. PMID:29243736
Targeting mutant p53 for efficient cancer therapy. PMID:29242642
Energy coupling mechanisms of AcrB-like RND transporters. PMID:29238744
Computer-Aided Drug Discovery in Plant Pathology. PMID:29238276
New algorithms to represent complex pseudoknotted RNA structures in dot-bracket notation. PMID:29236971
Unexpected Binding Mode of a Potent Indeno[1,2-b]indole-Type Inhibitor of Protein Kinase CK2 Revealed by Complex Structures with the Catalytic Subunit CK2α and Its Paralog CK2α'. PMID:29236079
BoBER: web interface to the base of bioisosterically exchangeable replacements. PMID:29234984
Mechanistic Insights into the Reaction of Chlorination of Tryptophan Catalyzed by Tryptophan 7-Halogenase. PMID:29234124
Compatible topologies and parameters for NMR structure determination of carbohydrates by simulated annealing. PMID:29232406
Structure-based prediction of ligand-protein interactions on a genome-wide scale. PMID:29229851
DeepSF: deep convolutional neural network for mapping protein sequences to folds. PMID:29228193
Pockets as structural descriptors of EGFR kinase conformations. PMID:29228029
Molecular docking based screening of a simulated HIF-1 protein model for potential inhibitors. PMID:29225432
Diverse effects of distance cutoff and residue interval on the performance of distance-dependent atom-pair potential in protein structure prediction. PMID:29221443
AllerBase: a comprehensive allergen knowledgebase. PMID:29220458
Multi-field query expansion is effective for biomedical dataset retrieval. PMID:29220457
TIBLE: a web-based, freely accessible resource for small-molecule binding data for mycobacterial species. PMID:29220433
Protein 3D Structure and Electron Microscopy Map Retrieval Using 3D-SURFER2.0 and EM-SURFER. PMID:29220075
Prediction of protein-ligand interactions from paired protein sequence motifs and ligand substructures. PMID:29218866
Active-site plasticity revealed in the asymmetric dimer of AnPrx6 the 1-Cys peroxiredoxin and molecular chaperone from Anabaena sp. PCC 7210. PMID:29215017
Allosteric Control of a Plant Receptor Kinase through S-Glutathionylation. PMID:29211989
Synthesis and preliminary structure-activity relationship study of 2-aryl-2H-pyrazolo[4,3-c]quinolin-3-ones as potential checkpoint kinase 1 (Chk1) inhibitors. PMID:29210298
X-ray diffraction reveals the intrinsic difference in the physical properties of membrane and soluble proteins. PMID:29208950
Polymer Informatics: Opportunities and Challenges. PMID:29201535
Structure-based pharmacophore design and virtual screening for novel potential inhibitors of epidermal growth factor receptor as an approach to breast cancer chemotherapy. PMID:29197962
Rapid and reliable protein structure determination via chemical shift threading. PMID:29196969
Direct regulation of p190RhoGEF by activated Rho and Rac GTPases. PMID:29196061
On the helical arrangements of protein molecules. PMID:29194829
Bioactive focus in conformational ensembles: a pluralistic approach. PMID:29189937
On the Early Evolution of Catabolic Pathways: A Comparative Genomics Approach. I. The Cases of Glucose, Ribose, and the Nucleobases Catabolic Routes. PMID:29189888
PON-SC - program for identifying steric clashes caused by amino acid substitutions. PMID:29187139
Protein Kinase Targets in Breast Cancer. PMID:29186886
Identifying the Epitope Regions of Therapeutic Antibodies Based on Structure Descriptors. PMID:29186775
Intrinsic Disorder in Proteins with Pathogenic Repeat Expansions. PMID:29186753
Crystal structure of an anti-CRISPR protein, AcrIIA1. PMID:29182776
Varieties of charge distributions in coat proteins of ssRNA+ viruses. PMID:29182522
Features of reactive cysteines discovered through computation: from kinase inhibition to enrichment around protein degrons. PMID:29180682
Template-based quaternary structure prediction of proteins using enhanced profile-profile alignments. PMID:29178285
Validation of Structures in the Protein Data Bank. PMID:29174494
Sequence analysis of the N-acetyltransferase 2 gene (NAT2) among Jordanian volunteers. PMID:29173142
Identification and analysis of seven effector protein families with different adaptive and evolutionary histories in plant-associated members of the Xanthomonadaceae. PMID:29170530
Efficient conformational ensemble generation of protein-bound peptides. PMID:29168051
Structural analyses of adenylate kinases from Antarctic and tropical fishes for understanding cold adaptation of enzymes. PMID:29167503
Conformational Dynamics of Asparagine at Coiled-Coil Interfaces. PMID:29166010
Expanding the repertoire of DNA shape features for genome-scale studies of transcription factor binding. PMID:29165643
Targeting Dengue Virus NS-3 Helicase by Ligand based Pharmacophore Modeling and Structure based Virtual Screening. PMID:29164104
Quantitative first principles calculations of protein circular dichroism in the near-ultraviolet. PMID:29163925
Selection of Amino Acid Chirality via Neutrino Interactions with 14N in Crossed Electric and Magnetic Fields. PMID:29160728
Determination of Hydrophobic Lengths of Membrane Proteins with the HDGB Implicit Membrane Model. PMID:29155578
PDB-wide identification of biological assemblies from conserved quaternary structure geometry. PMID:29155427
Monoamine oxidases inhibitors from Colvillea racemosa: Isolation, biological evaluation, and computational study. PMID:29154867
Quantitative high-throughput screening identifies cytoprotective molecules that enhance SUMO conjugation via the inhibition of SUMO-specific protease (SENP)2. PMID:29146736
Docking-based Screening of Ficus religiosa Phytochemicals as Inhibitors of Human Histamine H2 Receptor. PMID:29142437
Millisecond dynamics of BTK reveal kinome-wide conformational plasticity within the apo kinase domain. PMID:29142210
Emergence of Double- and Triple-Gene Reassortant G1P[8] Rotaviruses Possessing a DS-1-Like Backbone after Rotavirus Vaccine Introduction in Malawi. PMID:29142125
SuperDRUG2: a one stop resource for approved/marketed drugs. PMID:29140469
Targeting SxIP-EB1 interaction: An integrated approach to the discovery of small molecule modulators of dynamic binding sites. PMID:29138501
Structure-function relationships in ABCG2: insights from molecular dynamics simulations and molecular docking studies. PMID:29138424
The eukaryotic linear motif resource - 2018 update. PMID:29136216
Fluorescently-tagged human eIF3 for single-molecule spectroscopy. PMID:29136179
Sequential search leads to faster, more efficient fragment-based de novo protein structure prediction. PMID:29136098
Hydrogen/deuterium exchange mass spectrometry and computational modeling reveal a discontinuous epitope of an antibody/TL1A Interaction. PMID:29135326
Random protein sequences can form defined secondary structures and are well-tolerated in vivo. PMID:29133927
Unraveling the key to the resistance of canids to prion diseases. PMID:29131852
Excessive aggregation of membrane proteins in the Martini model. PMID:29131844
Excessive aggregation of membrane proteins in the Martini model. PMID:29131844
Acebutolol, a Cardioselective Beta Blocker, Promotes Glucose Uptake in Diabetic Model Cells by Inhibiting JNK-JIP1 Interaction. PMID:29129046
Lessons learned in induced fit docking and metadynamics in the Drug Design Data Resource Grand Challenge 2. PMID:29127581
PDBe: towards reusable data delivery infrastructure at protein data bank in Europe. PMID:29126160
Comprehensive analysis of the dynamic structure of nuclear localization signals. PMID:29124229
Structure-based pKa prediction provides a thermodynamic basis for the role of histidines in pH-induced conformational transitions in dengue virus. PMID:29124227
Analysis of the conformations of the HIV-1 protease from a large crystallographic data set. PMID:29124093
Similar Active Sites and Mechanisms Do Not Lead to Cross-Promiscuity in Organophosphate Hydrolysis: Implications for Biotherapeutic Engineering. PMID:29113434
Design, Synthesis, Biological Evaluation, and X-ray Studies of HIV-1 Protease Inhibitors with Modified P2' Ligands of Darunavir. PMID:29110408
miPepBase: A Database of Experimentally Verified Peptides Involved in Molecular Mimicry. PMID:29109711
Engineering of a membrane-triggered activity switch in coagulation factor VIIa. PMID:29109275
Base pair probability estimates improve the prediction accuracy of RNA non-canonical base pairs. PMID:29107980
Molecular Dynamics Simulation Reveals Specific Interaction Sites between Scorpion Toxins and Kv1.2 Channel: Implications for Design of Highly Selective Drugs. PMID:29104247
Enhancing the Thermostability of Rhizomucor miehei Lipase with a Limited Screening Library by Rational-Design Point Mutations and Disulfide Bonds. PMID:29101200
Diaryl ethers with carboxymethoxyphenacyl motif as potent HIV-1 reverse transcriptase inhibitors with improved solubility. PMID:29098886
KIXBASE: A comprehensive web resource for identification and exploration of KIX domains. PMID:29097748
Pink-beam serial crystallography. PMID:29097720
Specific and intrinsic sequence patterns extracted by deep learning from intra-protein binding and non-binding peptide fragments. PMID:29097708
GRAFENE: Graphlet-based alignment-free network approach integrates 3D structural and sequence (residue order) data to improve protein structural comparison. PMID:29097661
Computational design of membrane proteins using RosettaMembrane. PMID:29090504
Molecular Insight into the Acryloyl-CoA Hydration by AcuH for Acrylate Detoxification in Dimethylsulfoniopropionate-Catabolizing Bacteria. PMID:29089943
Synthesis and Biological Evaluation of 2H-Indazole Derivatives: Towards Antimicrobial and Anti-Inflammatory Dual Agents. PMID:29088121
STCRDab: the structural T-cell receptor database. PMID:29087479
chemalot and chemalot_knime: Command line programs as workflow tools for drug discovery. PMID:29086196
Open chemistry: RESTful web APIs, JSON, NWChem and the modern web application. PMID:29086154
Searching for bioactive conformations of drug-like ligands with current force fields: how good are we? PMID:29086109
Data driven polypharmacological drug design for lung cancer: analyses for targeting ALK, MET, and EGFR. PMID:29086093
Scoria: a Python module for manipulating 3D molecular data. PMID:29086076
Hydrogen Bond Variations of Influenza A Viruses During Adaptation in Human. PMID:29085020
Sequence-based prediction of permissive stretches for internal protein tagging and knockdown. PMID:29084520
One Novel 2.43Kb Deletion and One Single Nucleotide Mutation of the INSR Gene in a Chinese Neonate with Rabson-Mendenhall Syndrome. PMID:29082893
Vaccinomics Approach for Designing Potential Peptide Vaccine by Targeting Shigella spp. Serine Protease Autotransporter Subfamily Protein SigA. PMID:29082265
Keeping it complicated: Mitochondrial genome plasticity across diplonemids. PMID:29074957
Evidence of evolutionary selection for cotranslational folding. PMID:29073068
Self-association of a highly charged arginine-rich cell-penetrating peptide. PMID:29073067
Molecular Dynamics Simulations and Dynamic Network Analysis Reveal the Allosteric Unbinding of Monobody to H-Ras Triggered by R135K Mutation. PMID:29072601
Assessment of protein assembly prediction in CASP12. PMID:29071742
RCSB Protein Data Bank: Sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education. PMID:29067736
Molecular Skin Surface-Based Transformation Visualization between Biological Macromolecules. PMID:29065609
Coumestrol Epigenetically Suppresses Cancer Cell Proliferation: Coumestrol Is a Natural Haspin Kinase Inhibitor. PMID:29064398
Molecular docking and simulation studies of Phyllanthus amarus phytocompounds against structural and nucleocapsid proteins of white spot syndrome virus. PMID:29062674
LCS-TA to identify similar fragments in RNA 3D structures. PMID:29058576
Chiglitazar Preferentially Regulates Gene Expression via Configuration-Restricted Binding and Phosphorylation Inhibition of PPARγ. PMID:29056962
Differential Interaction of Antimicrobial Peptides with Lipid Structures Studied by Coarse-Grained Molecular Dynamics Simulations. PMID:29053635
Comparing pharmacophore models derived from crystallography and NMR ensembles. PMID:29047011
What do docking and QSAR tell us about the design of HIV-1 reverse transcriptase nonnucleoside inhibitors? PMID:29046967
Interpreting T-Cell Cross-reactivity through Structure: Implications for TCR-Based Cancer Immunotherapy. PMID:29046675
HpARI Protein Secreted by a Helminth Parasite Suppresses Interleukin-33. PMID:29045903
Machine learning accelerates MD-based binding pose prediction between ligands and proteins. PMID:29040432
Packing topology in crystals of proteins and small molecules: a comparison. PMID:29038549
Decrypting Strong and Weak Single-Walled Carbon Nanotubes Interactions with Mitochondrial Voltage-Dependent Anion Channels Using Molecular Docking and Perturbation Theory. PMID:29038520
In silico analysis of putative drug and vaccine targets of the metabolic pathways of Actinobacillus pleuropneumoniae using a subtractive/comparative genomics approach. PMID:29032659
Effect of single-residue bulges on RNA double-helical structures: crystallographic database analysis and molecular dynamics simulation studies. PMID:29032448
RNA Regulations and Functions Decoded by Transcriptome-wide RNA Structure Probing. PMID:29031843
Herbacetin suppresses cutaneous squamous cell carcinoma and melanoma cell growth by targeting AKT and ODC. PMID:29029040
Review of computational methods for virus-host protein interaction prediction: a case study on novel Ebola-human interactions. PMID:29028879
Self-assembly of model proteins into virus capsids. PMID:29027904
The role of the glycosyl moiety of myricetin derivatives in anti-HIV-1 activity in vitro. PMID:29025433
Extending the Nonbonded Cationic Dummy Model to Account for Ion-Induced Dipole Interactions. PMID:29022713
Predictive Structure-Based Toxicology Approaches To Assess the Androgenic Potential of Chemicals. PMID:29022712
Protein-protein interactions in paralogues: Electrostatics modulates specificity on a conserved steric scaffold. PMID:29016650
Biochemical and Structural Characterization of the Carbohydrate Transport Substrate-binding-protein SP0092. PMID:28994793
Reassessing the Structure and Function Relationship of the O2 Sensing Transcription Factor FNR. PMID:28990402
Enhanced unbiased sampling of protein dynamics using evolutionary coupling information. PMID:28983093
Hybrid approach to structure modeling of the histamine H3 receptor: Multi-level assessment as a tool for model verification. PMID:28982153
The Encyclopedia of Proteome Dynamics: a big data ecosystem for (prote)omics. PMID:28981707
Coupling X-Ray Reflectivity and In Silico Binding to Yield Dynamics of Membrane Recognition by Tim1. PMID:28978444
pH Dependence of Charge Multipole Moments in Proteins. PMID:28978439
Computational Macrocyclization: From de novo Macrocycle Generation to Binding Affinity Estimation. PMID:28977738
Characterization and Trypanocidal Activity of a Novel Pyranaphthoquinone. PMID:28973960
Chemical substitutions in the selectivity filter of potassium channels do not rule out constricted-like conformations for C-type inactivation. PMID:28973956
Decomposing protein-DNA binding and recognition using simplified protein models. PMID:28973439
Elucidating the 3D structures of Al(iii)-Aβ complexes: a template free strategy based on the pre-organization hypothesis. PMID:28970891
HUMA: A platform for the analysis of genetic variation in humans. PMID:28967693
Quasiharmonic analysis of protein energy landscapes from pressure-temperature molecular dynamics simulations. PMID:28964004
Sequence composition predicts immunoglobulin superfamily members that could share the intrinsically disordered properties of antibody CH1 domains. PMID:28963509
Tools for the cryo-EM gold rush: going from the cryo-EM map to the atomistic model. PMID:28963369
Integrative structure modeling with the Integrative Modeling Platform. PMID:28960548
Accelerating physical simulations of proteins by leveraging external knowledge. PMID:28959358
Variability of the Cyclin-Dependent Kinase 2 Flexibility Without Significant Change in the Initial Conformation of the Protein or Its Environment; a Computational Study. PMID:28959320
Structural Basis for EarP-Mediated Arginine Glycosylation of Translation Elongation Factor EF-P. PMID:28951478
γ-Carboxymuconolactone decarboxylase: a novel cell cycle-related basal body protein in the early branching eukaryote Trichomonas vaginalis. PMID:28950916
A single point mutation in a TssB/VipA homolog disrupts sheath formation in the type VI secretion system of Proteus mirabilis. PMID:28949977
Iterative Molecular Dynamics-Rosetta Membrane Protein Structure Refinement Guided by Cryo-EM Densities. PMID:28949136
Spatial distribution of disease-associated variants in three-dimensional structures of protein complexes. PMID:28945216
Intermolecular interactions involving an acidic patch on immunoglobulin variable domain and the γ2 constant region mediate crystalline inclusion body formation in the endoplasmic reticulum. PMID:28944095
In silico analysis of binding interaction of conantokins with NMDA receptors for potential therapeutic use in Alzheimer's disease. PMID:28943883
Redox state-dependent modulation of plant SnRK1 kinase activity differs from AMPK regulation in animals. PMID:28940407
Customizable de novo design strategies for DOCK: Application to HIVgp41 and other therapeutic targets. PMID:28940386
Novel FXa Inhibitor Identification through Integration of Ligand- and Structure-Based Approaches. PMID:28937618
Combining asymmetric 13C-labeling and isotopic filter/edit NOESY: a novel strategy for rapid and logical RNA resonance assignment. PMID:28934505
SupeRNAlign: a new tool for flexible superposition of homologous RNA structures and inference of accurate structure-based sequence alignments. PMID:28934487
Design and Structure-Guided Development of Novel Inhibitors of the Xeroderma Pigmentosum Group A (XPA) Protein-DNA Interaction. PMID:28933851
α-Glucosidase inhibition by flavonoids: an in vitro and in silico structure-activity relationship study. PMID:28933564
Survey of Predictors of Propensity for Protein Production and Crystallization with Application to Predict Resolution of Crystal Structures. PMID:28933304
Computational Analysis of Gynura bicolor Bioactive Compounds as Dipeptidyl Peptidase-IV Inhibitor. PMID:28932239
An iterative compound screening contest method for identifying target protein inhibitors using the tyrosine-protein kinase Yes. PMID:28931921
Energetics and mechanism of anion permeation across formate-nitrite transporters. PMID:28931899
Vermont: a multi-perspective visual interactive platform for mutational analysis. PMID:28929973
Pyrophosphate Release in the Protein HIV Reverse Transcriptase. PMID:28926712
Computational Analysis of Gynura bicolor Bioactive Compounds as Dipeptidyl Peptidase-IV Inhibitor. PMID:28932239
An iterative compound screening contest method for identifying target protein inhibitors using the tyrosine-protein kinase Yes. PMID:28931921
Energetics and mechanism of anion permeation across formate-nitrite transporters. PMID:28931899
Vermont: a multi-perspective visual interactive platform for mutational analysis. PMID:28929973
Pyrophosphate Release in the Protein HIV Reverse Transcriptase. PMID:28926712
A network integration approach for drug-target interaction prediction and computational drug repositioning from heterogeneous information. PMID:28924171
Deep learning methods for protein torsion angle prediction. PMID:28923002
Development of constant-pH simulation methods in implicit solvent and applications in biomolecular systems. PMID:28921104
A Multidirectional Perspective for Novel Functional Products: In vitro Pharmacological Activities and In silico Studies on Ononis natrix subsp. hispanica. PMID:28919860
Limiting Values of the one-bond C-H Spin-Spin Coupling Constants of the Imidazole Ring of Histidine at High-pH. PMID:28919647
Optimal affinity ranking for automated virtual screening validated in prospective D3R grand challenges. PMID:28918599
Practical computational toolkits for dendrimers and dendrons structure design. PMID:28916961
Structural and Dynamics Perspectives on the Binding of Substrate and Inhibitors in Mycobacterium tuberculosis DHFR. PMID:28914808
Predicting the affinity of Farnesoid X Receptor ligands through a hierarchical ranking protocol: a D3R Grand Challenge 2 case study. PMID:28913743
Performance of multiple docking and refinement methods in the pose prediction D3R prospective Grand Challenge 2016. PMID:28913710
Global organization of a binding site network gives insight into evolution and structure-function relationships of proteins. PMID:28912495
Systematic Mutagenesis of Serine Hydroxymethyltransferase Reveals an Essential Role in Nematode Resistance. PMID:28912378
The eBioKit, a stand-alone educational platform for bioinformatics. PMID:28910280
Structural insights into leishmanolysins encoded on chromosome 10 of Leishmania (Viannia) braziliensis. PMID:28902287
Interactive comparison and remediation of collections of macromolecular structures. PMID:28901593
The SubCons webserver: A user friendly web interface for state-of-the-art subcellular localization prediction. PMID:28901589
Bioinformatics analysis of genetic variants of endoplasmic reticulum aminopeptidase 1 in ankylosing spondylitis. PMID:28901420
From malaria to cancer: Computational drug repositioning of amodiaquine using PLIP interaction patterns. PMID:28900272
Exploring the inhibition mechanism of adenylyl cyclase type 5 by n-terminal myristoylated Gαi1. PMID:28892485
COX Inhibition Profile and Molecular Docking Studies of Some 2-(Trimethoxyphenyl)-Thiazoles. PMID:28891941
Structural analyses of the Haemophilus influenzae peptidoglycan synthase activator LpoA suggest multiple conformations in solution. PMID:28887305
Deep learning-based subdivision approach for large scale macromolecules structure recovery from electron cryo tomograms. PMID:28881965
APIO-EE-9 is a novel Aurora A and B antagonist that suppresses esophageal cancer growth in a PDX mouse model. PMID:28881819
Association of high microvessel αvβ3 and low PTEN with poor outcome in stage 3 neuroblastoma: rationale for using first in class dual PI3K/BRD4 inhibitor, SF1126. PMID:28881723
Molecular modeling and structure-based drug discovery approach reveals protein kinases as off-targets for novel anticancer drug RH1. PMID:28879492
Identification of the Tolfenamic Acid Binding Pocket in PrbP from Liberibacter asiaticus. PMID:28878750
A Protocol for Generating and Exchanging (Genome-Scale) Metabolic Resource Allocation Models. PMID:28878200
PDBsum: Structural summaries of PDB entries. PMID:28875543
Rational design of drug-like compounds targeting Mycobacterium marinum MelF protein. PMID:28873466
Potential Roles of Intrinsic Disorder in Maternal-Effect Proteins Involved in the Maintenance of DNA Methylation. PMID:28869544
Differences in Sulfotyrosine Binding amongst CXCR1 and CXCR2 Chemokine Ligands. PMID:28869519
Probing the modulated formation of gold nanoparticles-beta-lactoglobulin corona complexes and their applications. PMID:28869274
An Unusual Dimeric Inhibitor of Acetylcholinesterase: Cooperative Binding of Crystal Violet. PMID:28867801
High-Resolution Cryo-EM Maps and Models: A Crystallographer's Perspective. PMID:28867613
Instant Construction and Visualization of Crowded Biological Environments. PMID:28866533
Blinded evaluation of farnesoid X receptor (FXR) ligands binding using molecular docking and free energy calculations. PMID:28865056
Protein-Protein Interactions in Virus-Host Systems. PMID:28861068
A membrane-inserted structural model of the yeast mitofusin Fzo1. PMID:28860650
Protoplast Swelling and Hypocotyl Growth Depend on Different Auxin Signaling Pathways. PMID:28860155
FGFR2 regulation by picrasidine Q inhibits the cell growth and induces apoptosis in esophageal squamous cell carcinoma. PMID:28857247
Polycipiviridae: a proposed new family of polycistronic picorna-like RNA viruses. PMID:28857036
Expression, Docking, and Molecular Dynamics of Endo-β-1,4-xylanase I Gene of Trichoderma virens in Pichia stipitis. PMID:28856159
The molecular basis for peptide repertoire selection in the human leucocyte antigen (HLA) C*06:02 molecule. PMID:28855257
EL_PSSM-RT: DNA-binding residue prediction by integrating ensemble learning with PSSM Relation Transformation. PMID:28851273
Interaction of factor V B-domain acidic region with its basic region and with TFPI/TFPI2: Structural insights from molecular modeling studies. PMID:28845483
MDplot: Visualise Molecular Dynamics. PMID:28845302
Picomolar inhibition of β-galactosidase (bovine liver) attributed to loop closure. PMID:28844803
Two CYP82D Enzymes Function as Flavone Hydroxylases in the Biosynthesis of Root-Specific 4'-Deoxyflavones in Scutellaria baicalensis. PMID:28842248
Combining self- and cross-docking as benchmark tools: the performance of DockBench in the D3R Grand Challenge 2. PMID:28840418
Bis-spirochromanones as potent inhibitors of Mycobacterium tuberculosis: synthesis and biological evaluation. PMID:28840414
Fungal Hybrid B heme peroxidases - unique fusions of a heme peroxidase domain with a carbohydrate-binding domain. PMID:28839281
Effects of short indels on protein structure and function in human genomes. PMID:28839204
A systematic analysis of the RNA-targeting potential of secreted bacterial effector proteins. PMID:28839189
Chelation and stabilization of berkelium in oxidation state +IV. PMID:28837177
Looking Back, Looking Forward at Halogen Bonding in Drug Discovery. PMID:28837116
A cross docking pipeline for improving pose prediction and virtual screening performance. PMID:28836076
The Enigmatic Origin of Papillomavirus Protein Domains. PMID:28832519
Performance of HADDOCK and a simple contact-based protein-ligand binding affinity predictor in the D3R Grand Challenge 2. PMID:28831657
Structure-activity relationships and molecular docking studies of chromene and chromene based azo chromophores: A novel series of potent antimicrobial and anticancer agents. PMID:28828001
Mutagenesis of the NaChBac sodium channel discloses a functional role for a conserved S6 asparagine. PMID:28825121
Alkaline Phosphatase, an Unconventional Immune Protein. PMID:28824625
Promiscuity, impersonation and accommodation: evolution of plant specialized metabolism. PMID:28822280
Data-driven coarse graining of large biomolecular structures. PMID:28817608
Exploring the potential of a structural alphabet-based tool for mining multiple target conformations and target flexibility insight. PMID:28817602
Physics-based all-atom modeling of RNA energetics and structure. PMID:28815951
Molstack-Interactive visualization tool for presentation, interpretation, and validation of macromolecules and electron density maps. PMID:28815771
Prediction of Reduction Potentials of Copper Proteins with Continuum Electrostatics and Density Functional Theory. PMID:28815759
Endolysosomal Degradation of Allergenic Ole e 1-Like Proteins: Analysis of Proteolytic Cleavage Sites Revealing T Cell Epitope-Containing Peptides. PMID:28812992
eDGAR: a database of Disease-Gene Associations with annotated Relationships among genes. PMID:28812536
NSiteMatch: Prediction of Binding Sites of Nucleotides by Identifying the Structure Similarity of Local Surface Patches. PMID:28811833
Joint inflammation related citrullination of functional arginines in extracellular proteins. PMID:28811641
Effects of Cations on the Behaviour of Lipid Cubic Phases. PMID:28811541
A combinatorial approach for the discovery of cytochrome P450 2D6 inhibitors from nature. PMID:28808272
SpotOn: High Accuracy Identification of Protein-Protein Interface Hot-Spots. PMID:28808256
Navigating the conformational landscape of G protein-coupled receptor kinases during allosteric activation. PMID:28808053
Function of Novel Anti-CD19 Chimeric Antigen Receptors with Human Variable Regions Is Affected by Hinge and Transmembrane Domains. PMID:28807568
In silico structure-based approaches to discover protein-protein interaction-targeting drugs. PMID:28802714
Utility of rapid whole-exome sequencing in the diagnosis of Niemann-Pick disease type C presenting with fetal hydrops and acute liver failure. PMID:28802248
Cyclic oligomer design with de novo αβ-proteins. PMID:28801928
POVME 3.0: Software for Mapping Binding Pocket Flexibility. PMID:28800393
Protein structure prediction: making AWSEM AWSEM-ER by adding evolutionary restraints. PMID:28799172
The quinic acid derivative KZ-41 prevents glucose-induced caspase-3 activation in retinal endothelial cells through an IGF-1 receptor dependent mechanism. PMID:28796787
The Adaptive Evolution Database (TAED): A New Release of a Database of Phylogenetically Indexed Gene Families from Chordates. PMID:28795237
Structure-Based Design of Hepatitis C Virus Vaccines That Elicit Neutralizing Antibody Responses to a Conserved Epitope. PMID:28794021
Gaussian network model can be enhanced by combining solvent accessibility in proteins. PMID:28790346
Computational-experimental approach to drug-target interaction mapping: A case study on kinase inhibitors. PMID:28787438
Origins of coevolution between residues distant in protein 3D structures. PMID:28784799
Inhibition of glutamate decarboxylase (GAD) by ethyl ketopentenoate (EKP) induces treatment-resistant epileptic seizures in zebrafish. PMID:28775328
In silico model of the human ClC-Kb chloride channel: pore mapping, biostructural pathology and drug screening. PMID:28775266
B3GAT3-related disorder with craniosynostosis and bone fragility due to a unique mutation. PMID:28771243
Adsorption of Milk Proteins (β-Casein and β-Lactoglobulin) and BSA onto Hydrophobic Surfaces. PMID:28767100
Various Mechanisms Involve the Nuclear Factor (Erythroid-Derived 2)-Like (NRF2) to Achieve Cytoprotection in Long-Term Cisplatin-Treated Urothelial Carcinoma Cell Lines. PMID:28767070
Ranking docking poses by graph matching of protein-ligand interactions: lessons learned from the D3R Grand Challenge 2. PMID:28766097
EMQIT: a machine learning approach for energy based PWM matrix quality improvement. PMID:28764727
Functional optimization of agonistic antibodies to OX40 receptor with novel Fc mutations to promote antibody multimerization. PMID:28758875
All-Atom MD Predicts Magnesium-Induced Hairpin in Chemically Perturbed RNA Analog of F10 Therapeutic. PMID:28745046
Capturing protein communities by structural proteomics in a thermophilic eukaryote. PMID:28743795
Mechanisms and Specificity of Phenazine Biosynthesis Protein PhzF. PMID:28740244
The Dark Proteome Database. PMID:28736578
β-Ginkgotides: Hyperdisulfide-constrained peptides from Ginkgo biloba. PMID:28733600
Lead(II) Binding in Natural and Artificial Proteins. PMID:28731303
3D-QSAR studies on Maslinic acid analogs for Anticancer activity against Breast Cancer cell line MCF-7. PMID:28729623
Machine learning-enabled discovery and design of membrane-active peptides. PMID:28728899
ProtozoaDB 2.0: A Trypanosoma Brucei Case Study. PMID:28726736
Molecular mechanisms involved in the side effects of fatty acid amide hydrolase inhibitors: a structural phenomics approach to proteome-wide cellular off-target deconvolution and disease association. PMID:28725477
Reciprocal carbonyl-carbonyl interactions in small molecules and proteins. PMID:28724906
Flexible small molecular anti-estrogens with N,N-dialkylated-2,5-diethoxy-4-morpholinoaniline scaffold targets multiple estrogen receptor conformations. PMID:28723234
Beta-lactamase database (BLDB) - structure and function. PMID:28719998
Serum Albumin Binding and Esterase Activity: Mechanistic Interactions with Organophosphates. PMID:28718803
Protein-protein binding selectivity and network topology constrain global and local properties of interface binding networks. PMID:28717235
Comparing NMR and X-ray protein structure: Lindemann-like parameters and NMR disorder. PMID:28714803
Evaluation of Selected CYP51A1 Polymorphisms in View of Interactions with Substrate and Redox Partner. PMID:28713270
ATP binding and hydrolysis disrupt the high-affinity interaction between the heme ABC transporter HmuUV and its cognate substrate-binding protein. PMID:28710276
The enigma of the near-symmetry of proteins: Domain swapping. PMID:28708874
Neutron crystallographic studies of T4 lysozyme at cryogenic temperature. PMID:28707382
Methionine synthase is localized to the nucleus in Pichia pastoris and Candida albicans and to the cytoplasm in Saccharomyces cerevisiae. PMID:28701466
Comparison of Protein Extracts from Various Unicellular Green Sources. PMID:28701042
Computational and Experimental Studies of ADP-Ribosylation. PMID:28695527
Identifying and Validating Tankyrase Binders and Substrates: A Candidate Approach. PMID:28695526
Competitive rational inhibitor design to 4-maleylaceto-acetate isomerase. PMID:28690379
Accelerating smooth molecular surface calculation. PMID:28689219
Usage of a dataset of NMR resolved protein structures to test aggregation versus solubility prediction algorithms. PMID:28685932
Enzyme Architecture: Modeling the Operation of a Hydrophobic Clamp in Catalysis by Triosephosphate Isomerase. PMID:28683550
Host association and selection on salivary protein genes in bed bugs and related blood-feeding ectoparasites. PMID:28680688
Molecular Simulations of Carbohydrates with a Fucose-Binding Burkholderia ambifaria Lectin Suggest Modulation by Surface Residues Outside the Fucose-Binding Pocket. PMID:28680402
Functional validation reveals the novel missense V419L variant in TGFBR2 associated with Loeys-Dietz syndrome (LDS) impairs canonical TGF-β signaling. PMID:28679693
Crystal structures of agonist-bound human cannabinoid receptor CB1. PMID:28678776
In silico Study of the Pharmacologic Properties and Cytotoxicity Pathways in Cancer Cells of Various Indolylquinone Analogues of Perezone. PMID:28672837
Improving binding mode and binding affinity predictions of docking by ligand-based search of protein conformations: evaluation in D3R grand challenge 2015. PMID:28668990
Conformational Heterogeneity of the HIV Envelope Glycan Shield. PMID:28667249
DNM1 encephalopathy: A new disease of vesicle fission. PMID:28667181
MDD-Palm: Identification of protein S-palmitoylation sites with substrate motifs based on maximal dependence decomposition. PMID:28662047
Do Halogen-Hydrogen Bond Donor Interactions Dominate the Favorable Contribution of Halogens to Ligand-Protein Binding? PMID:28657759
Antibody against Microbial Neuraminidases Recognizes Human Sialidase 3 (NEU3): the Neuraminidase/Sialidase Superfamily Revisited. PMID:28655817
Structure-Based Design and Synthesis of Potent and Selective Matrix Metalloproteinase 13 Inhibitors. PMID:28653849
Resurrecting the Dead (Molecules). PMID:28652896
Targeting the Homoserine Dehydrogenase of Paracoccidioides Species for Treatment of Systemic Fungal Infections. PMID:28652239
An L-threonine transaldolase is required for L-threo-β-hydroxy-α-amino acid assembly during obafluorin biosynthesis. PMID:28649989
Structural and regulatory diversity shape HLA-C protein expression levels. PMID:28649982
Role of inhibitors of serine peptidases in protecting Leishmania donovani against the hydrolytic peptidases of sand fly midgut. PMID:28645315
Can the propensity of protein crystallization be increased by using systematic screening with metals? PMID:28643473
Paralog-divergent Features May Help Reduce Off-target Effects of Drugs: Hints from Glucagon Subfamily Analysis. PMID:28642113
CompAnnotate: a comparative approach to annotate base-pairing interactions in RNA 3D structures. PMID:28641399
Peptide-Protein Binding Investigated by Far-IR Spectroscopy and Molecular Dynamics Simulations. PMID:28636914
Identifying specificity groups in the T cell receptor repertoire. PMID:28636589
The small GTPases K-Ras, N-Ras, and H-Ras have distinct biochemical properties determined by allosteric effects. PMID:28630043
3D deep convolutional neural networks for amino acid environment similarity analysis. PMID:28615003
Accurate prediction of functional effects for variants by combining gradient tree boosting with optimal neighborhood properties. PMID:28614374
"Martinizing" the Variational Implicit Solvent Method (VISM): Solvation Free Energy for Coarse-Grained Proteins. PMID:28613904
To be disordered or not to be disordered: is that still a question for proteins in the cell? PMID:28612216
Distribution of dipeptides in different protein structural classes: an effort to find new similarities. PMID:28612124
Structural and dynamic insights into the role of conformational switching in the nuclease activity of the Xanthomonas albilineans Cas2 in CRISPR-mediated adaptive immunity. PMID:28612041
Structural and Functional Insights into WRKY3 and WRKY4 Transcription Factors to Unravel the WRKY-DNA (W-Box) Complex Interaction in Tomato (Solanum lycopersicum L.). A Computational Approach. PMID:28611792
Molecular structures guide the engineering of chromatin. PMID:28609787
MiSynPat: An integrated knowledge base linking clinical, genetic, and structural data for disease-causing mutations in human mitochondrial aminoacyl-tRNA synthetases. PMID:28608363
Novel Class IIa-Selective Histone Deacetylase Inhibitors Discovered Using an in Silico Virtual Screening Approach. PMID:28607401
Extension and validation of the GLYCAM force field parameters for modeling glycosaminoglycans. PMID:28603292
Treating ion distribution with Gaussian-based smooth dielectric function in DelPhi. PMID:28602026
An Alcaligenes strain emulates Bacillus thuringiensis producing a binary protein that kills corn rootworm through a mechanism similar to Cry34Ab1/Cry35Ab1. PMID:28596570
Plant pectin acetylesterase structure and function: new insights from bioinformatic analysis. PMID:28595570
Albumin (BSA) adsorption onto graphite stepped surfaces. PMID:28595417
Comprehensive review of methods for prediction of intrinsic disorder and its molecular functions. PMID:28589442
Molecular cloning, expression, and characterization of four novel thermo-alkaliphilic enzymes retrieved from a metagenomic library. PMID:28588643
On the Integration of In Silico Drug Design Methods for Drug Repurposing. PMID:28588497
Photosynthetic pigment-protein complexes as highly connected networks: implications for robust energy transport. PMID:28588417
Network Analysis Reveals the Recognition Mechanism for Dimer Formation of Bulb-type Lectins. PMID:28588265
GPCR-SSFE 2.0-a fragment-based molecular modeling web tool for Class A G-protein coupled receptors. PMID:28582569
Glycan Reader is improved to recognize most sugar types and chemical modifications in the Protein Data Bank. PMID:28582506
Synthesis of 2-Oxo-1, 2-Dihydroquinoline Chemotype with Multiple Attachment Points as Novel Screening Compounds for Drug Discovery. PMID:28580379
Large-Scale Prediction of Drug-Target Interaction: a Data-Centric Review. PMID:28577120
Comprehensive classification of the PIN domain-like superfamily. PMID:28575517
MMTF-An efficient file format for the transmission, visualization, and analysis of macromolecular structures. PMID:28574982
Nickel Sequestration by the Host-Defense Protein Human Calprotectin. PMID:28573847
Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive. PMID:28573592
Stereochemistry and Validation of Macromolecular Structures. PMID:28573590
Many Ways to Derivatize Macromolecules and Their Crystals for Phasing. PMID:28573580
EMBuilder: A Template Matching-based Automatic Model-building Program for High-resolution Cryo-Electron Microscopy Maps. PMID:28572576
Cavity Versus Ligand Shape Descriptors: Application to Urokinase Binding Pockets. PMID:28570103
Integrating macromolecular X-ray diffraction data with the graphical user interface iMosflm. PMID:28569763
Current status and future prospect of FSHD region gene 1. PMID:28569257
Discovery and Mechanistic Study of Benzamide Derivatives That Modulate Hepatitis B Virus Capsid Assembly. PMID:28566379
Numerical integration methods and layout improvements in the context of dynamic RNA visualization. PMID:28558664
A unique profilin-actin interface is important for malaria parasite motility. PMID:28552953
TomoMiner and TomoMinerCloud: A Software Platform for Large-Scale Subtomogram Structural Analysis. PMID:28552576
Fully automated antibody structure prediction using BIOVIA tools: Validation study. PMID:28542300
Solution structure of domain 1.1 of the σA factor from Bacillus subtilis is preformed for binding to the RNA polymerase core. PMID:28539362
CLMSVault: A Software Suite for Protein Cross-Linking Mass-Spectrometry Data Analysis and Visualization. PMID:28537071
Complementary Approaches to Existing Target Based Drug Discovery for Identifying Novel Drug Targets. PMID:28536394
Designing the Sniper: Improving Targeted Human Cytolytic Fusion Proteins for Anti-Cancer Therapy via Molecular Simulation. PMID:28536352
Structural and enzymatic insights into species-specific resistance to schistosome parasite drug therapy. PMID:28536265
An exhaustive survey of regular peptide conformations using a new metric for backbone handedness (h). PMID:28533975
RNA editing of SLC22A3 drives early tumor invasion and metastasis in familial esophageal cancer. PMID:28533408
Identification of a novel putative inhibitor of the Plasmodium falciparum purine nucleoside phosphorylase: exploring the purine salvage pathway to design new antimalarial drugs. PMID:28523625
HDOCK: a web server for protein-protein and protein-DNA/RNA docking based on a hybrid strategy. PMID:28521030
The alphabet of intrinsic disorder: II. Various roles of glutamic acid in ordered and intrinsically disordered proteins. PMID:28516010
MFDp2: Accurate predictor of disorder in proteins by fusion of disorder probabilities, content and profiles. PMID:28516009
The alphabet of intrinsic disorder: I. Act like a Pro: On the abundance and roles of proline residues in intrinsically disordered proteins. PMID:28516008
Improving theranostics in pancreatic cancer. PMID:28513912
Benchmarking a computational design method for the incorporation of metal ion-binding sites at symmetric protein interfaces. PMID:28513090
MOLS sampling and its applications in structural biophysics. PMID:28510038
Protein-RNA interactions: structural biology and computational modeling techniques. PMID:28510023
Supporting the Identification of Novel Fragment-Based Positive Allosteric Modulators Using a Supervised Molecular Dynamics Approach: A Retrospective Analysis Considering the Human A2A Adenosine Receptor as a Key Example. PMID:28509867
Fast iodide-SAD phasing for high-throughput membrane protein structure determination. PMID:28508075
In Vitro and In Silico Antidiabetic and Antimicrobial Evaluation of Constituents from Kickxia ramosissima (Nanorrhinum ramosissimum). PMID:28507520
Gain-of-function mutations in Aqp3a influence zebrafish pigment pattern formation through the tissue environment. PMID:28506994
Unveiling a novel transient druggable pocket in BACE-1 through molecular simulations: Conformational analysis and binding mode of multisite inhibitors. PMID:28505196
Dissecting physical structure of calreticulin, an intrinsically disordered Ca2+-buffering chaperone from endoplasmic reticulum. PMID:28504081
Across-proteome modeling of dimer structures for the bottom-up assembly of protein-protein interaction networks. PMID:28499419
CHARMM-GUI ligand reader and modeler for CHARMM force field generation of small molecules. PMID:28497616
Structure-function analysis of RBP-J-interacting and tubulin-associated (RITA) reveals regions critical for repression of Notch target genes. PMID:28487372
Class III Histidine Kinases: a Recently Accessorized Kinase Domain in Putative Modulators of Type IV Pilus-Based Motility. PMID:28484044
Interaction of Biliverdin Chromophore with Near-Infrared Fluorescent Protein BphP1-FP Engineered from Bacterial Phytochrome. PMID:28481303
Nuclear Magnetic Resonance Structure and Binding Studies of PqqD, a Chaperone Required in the Biosynthesis of the Bacterial Dehydrogenase Cofactor Pyrroloquinoline Quinone. PMID:28481092
Deciphering the Biochemical Pathway and Pharmacokinetic Study of Amyloid βeta-42 with Superparamagnetic Iron Oxide Nanoparticles (SPIONs) Using Systems Biology Approach. PMID:28478508
Discrimination of Native-like States of Membrane Proteins with Implicit Membrane-based Scoring Functions. PMID:28475346
I-TASSER-MR: automated molecular replacement for distant-homology proteins using iterative fragment assembly and progressive sequence truncation. PMID:28472524
DSSR-enhanced visualization of nucleic acid structures in Jmol. PMID:28472503
BepiPred-2.0: improving sequence-based B-cell epitope prediction using conformational epitopes. PMID:28472356
Crystal structure of the essential biotin-dependent carboxylase AccA3 from Mycobacterium tuberculosis. PMID:28469974
Prediction of HBF-0259 interactions with hepatitis B Virus receptors and surface antigen secretory factors. PMID:28466034
Small molecule inhibitors of mesotrypsin from a structure-based docking screen. PMID:28463992
In Vitro Evaluation of Antileishmanial Activity of Computationally Screened Compounds against Ascorbate Peroxidase To Combat Amphotericin B Drug Resistance. PMID:28461317
GASS-WEB: a web server for identifying enzyme active sites based on genetic algorithms. PMID:28459991
Co-occurring protein phosphorylation are functionally associated. PMID:28459814
Allergens of Blomia tropicalis: An Overview of Recombinant Molecules. PMID:28456805
TraitRateProp: a web server for the detection of trait-dependent evolutionary rate shifts in sequence sites. PMID:28453644
Large-scale detection of drug off-targets: hypotheses for drug repurposing and understanding side-effects. PMID:28449705
Equilibrium Ensembles for Insulin Folding from Bias-Exchange Metadynamics. PMID:28445749
Directional Force Originating from ATP Hydrolysis Drives the GroEL Conformational Change. PMID:28445748
Crystal structure-based discovery of a novel synthesized PARP1 inhibitor (OL-1) with apoptosis-inducing mechanisms in triple-negative breast cancer. PMID:28442756
ChloroKB: A Web Application for the Integration of Knowledge Related to Chloroplast Metabolic Network. PMID:28442501
Conformational dynamics of bacterial trigger factor in apo and ribosome-bound states. PMID:28437479
A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density. PMID:28436492
Constrained Photophysics of 5,7-dimethoxy-2,3,4,9-tetrahydro-1H-carbazol-1-one in the Bioenvironment of Serum Albumins: A Spectroscopic Endeavour Supported by Molecular Docking Analysis. PMID:28434063
In-Silico Drug discovery approach targeting receptor tyrosine kinase-like orphan receptor 1 for cancer treatment. PMID:28432357
DNAproDB: an interactive tool for structural analysis of DNA-protein complexes. PMID:28431131
ClusPro PeptiDock: efficient global docking of peptide recognition motifs using FFT. PMID:28430871
The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design. PMID:28430426
AAV-ID: A Rapid and Robust Assay for Batch-to-Batch Consistency Evaluation of AAV Preparations. PMID:28427840
Structural characterization of core-bradavidin in complex with biotin. PMID:28426764
Cloning retinoid and peroxisome proliferator-activated nuclear receptors of the Pacific oyster and in silico binding to environmental chemicals. PMID:28426724
Revealing Hidden Conformational Space of LOV Protein VIVID Through Rigid Residue Scan Simulations. PMID:28425502
Crystal structures of the NO sensor NsrR reveal how its iron-sulfur cluster modulates DNA binding. PMID:28425466
Cross-reactive dengue human monoclonal antibody prevents severe pathologies and death from Zika virus infections. PMID:28422757
Structure and characterization of a class 3B proline utilization A: Ligand-induced dimerization and importance of the C-terminal domain for catalysis. PMID:28420730
EigenTHREADER: analogous protein fold recognition by efficient contact map threading. PMID:28419258
Mutation of neuron-specific chromatin remodeling subunit BAF53b: rescue of plasticity and memory by manipulating actin remodeling. PMID:28416631
The pimeloyl-CoA synthetase BioW defines a new fold for adenylate-forming enzymes. PMID:28414711
Substrate Profiling and High Resolution Co-complex Crystal Structure of a Secreted C11 Protease Conserved across Commensal Bacteria. PMID:28414448
Parallel reorganization of protein function in the spindle checkpoint pathway through evolutionary paths in the fitness landscape that appear neutral in laboratory experiments. PMID:28410373
Biophysical Approaches Facilitate Computational Drug Discovery for ATP-Binding Cassette Proteins. PMID:28409029
Histone deacetylase inhibition modulates histone acetylation at gene promoter regions and affects genome-wide gene transcription in Schistosoma mansoni. PMID:28406899
Computational Identification and Characterization of a Promiscuous T-Cell Epitope on the Extracellular Protein 85B of Mycobacterium spp. for Peptide-Based Subunit Vaccine Design. PMID:28401156
Riboswitch diversity and distribution. PMID:28396576
Modeling disordered protein interactions from biophysical principles. PMID:28394890
Five Fatty Aldehyde Dehydrogenase Enzymes from Marinobacter and Acinetobacter spp. and Structural Insights into the Aldehyde Binding Pocket. PMID:28389542
Effect of APOL1 disease risk variants on APOL1 gene product. PMID:28385815
Bayesian Modeling of Biomolecular Assemblies with Cryo-EM Maps. PMID:28382301
Production of homogeneous glycoprotein with multisite modifications by an engineered N-glycosyltransferase mutant. PMID:28381551
Core Genes Evolve Rapidly in the Long-Term Evolution Experiment with Escherichia coli. PMID:28379360
Evaluation of the novel algorithm of flexible ligand docking with moveable target-protein atoms. PMID:28377797
Using structural knowledge in the protein data bank to inform the search for potential host-microbe protein interactions in sequence space: application to Mycobacterium tuberculosis. PMID:28376709
Visualization of Alternative Functional Configurations of Influenza Virus Hemagglutinin Facilitates Rapid Selection of Complementing Vaccines in Emergency Situations. PMID:28375167
PDB2CD visualises dynamics within protein structures. PMID:28374045
Structure-Based Target-Specific Screening Leads to Small-Molecule CaMKII Inhibitors. PMID:28371191
The NIH 3D Print Exchange: A Public Resource for Bioscientific and Biomedical 3D Prints. PMID:28367477
Selecting high-quality negative samples for effectively predicting protein-RNA interactions. PMID:28361676
A pair-conformation-dependent scoring function for evaluating 3D RNA-protein complex structures. PMID:28358834
HIVed, a knowledgebase for differentially expressed human genes and proteins during HIV infection, replication and latency. PMID:28358052
Protein Corona-Induced Modification of Silver Nanoparticle Aggregation in Simulated Gastric Fluid. PMID:28357114
Is Open Science the Future of Drug Development? PMID:28356902
Design, synthesis and pharmaco-toxicological assessment of 5-mercapto-1,2,4-triazole derivatives with antibacterial and antiproliferative activity. PMID:28350123
Systematic identification of phosphorylation-mediated protein interaction switches. PMID:28346509
Molecular basis of P450 OleTJE: an investigation of substrate binding mechanism and major pathways. PMID:28342136
Structure and mechanism of benzaldehyde dehydrogenase from Pseudomonas putida ATCC 12633, a member of the Class 3 aldehyde dehydrogenase superfamily. PMID:28338942
Superposition-free comparison and clustering of antibody binding sites: implications for the prediction of the nature of their antigen. PMID:28338016
Discovery of novel phthalimide analogs: Synthesis, antimicrobial and antitubercular screening with molecular docking studies. PMID:28337109
BioJava-ModFinder: identification of protein modifications in 3D structures from the Protein Data Bank. PMID:28334105
The aggregation of cytochrome C may be linked to its flexibility during refolding. PMID:28330101
Discovery of potential ALK inhibitors by virtual screening approach. PMID:28330089
Determining Cysteines Available for Covalent Inhibition Across the Human Kinome. PMID:28326775
Understanding the conservation patterns and molecular phylogenetics of human death receptors family through computational biology. PMID:28324447
Identification of potential inhibitor targeting enoyl-acyl carrier protein reductase (InhA) in Mycobacterium tuberculosis: a computational approach. PMID:28324429
In silico study on Penicillin derivatives and Cephalosporins for upper respiratory tract bacterial pathogens. PMID:28324428
Computational pipeline to identify and characterize functional mutations in ornithine transcarbamylase deficiency. PMID:28324312
Crystal structure of the catalytic domain of Clostridium perfringens neuraminidase in complex with a non-carbohydrate-based inhibitor, 2-(cyclohexylamino)ethanesulfonic acid. PMID:28315686
Nucleosome Histone Tail Conformation and Dynamics: Impacts of Lysine Acetylation and a Nearby Minor Groove Benzo[a]pyrene-Derived Lesion. PMID:28304160
Development of Bioinformatics Infrastructure for Genomics Research. PMID:28302555
Structure-Based Analysis of Single Nucleotide Variants in the Renin-Angiotensinogen Complex. PMID:28302554
Role of Structural Bioinformatics in Drug Discovery by Computational SNP Analysis: Analyzing Variation at the Protein Level. PMID:28302551
Recessive coding and regulatory mutations in FBLIM1 underlie the pathogenesis of chronic recurrent multifocal osteomyelitis (CRMO). PMID:28301468
Systems-level understanding of ethanol-induced stresses and adaptation in E. coli. PMID:28300180
Fine-tuning the extent and dynamics of binding cleft opening as a potential general regulatory mechanism in parvulin-type peptidyl prolyl isomerases. PMID:28300139
Molecular characterization and homology modeling of spermidine synthase from Synechococcus sp. PCC 7942. PMID:28299555
Impact of genetic variation on three dimensional structure and function of proteins. PMID:28296894
Role of Structural Bioinformatics in Drug Discovery by Computational SNP Analysis: Analyzing Variation at the Protein Level. PMID:28302551
Recessive coding and regulatory mutations in FBLIM1 underlie the pathogenesis of chronic recurrent multifocal osteomyelitis (CRMO). PMID:28301468
Systems-level understanding of ethanol-induced stresses and adaptation in E. coli. PMID:28300180
Fine-tuning the extent and dynamics of binding cleft opening as a potential general regulatory mechanism in parvulin-type peptidyl prolyl isomerases. PMID:28300139
Molecular characterization and homology modeling of spermidine synthase from Synechococcus sp. PCC 7942. PMID:28299555
Impact of genetic variation on three dimensional structure and function of proteins. PMID:28296894
The use of small-molecule structures to complement protein-ligand crystal structures in drug discovery. PMID:28291759
Traditionally Used Lathyrus Species: Phytochemical Composition, Antioxidant Activity, Enzyme Inhibitory Properties, Cytotoxic Effects, and in silico Studies of L. czeczottianus and L. nissolia. PMID:28289386
Characterization of Biomolecular Helices and Their Complementarity Using Geometric Analysis. PMID:28287728
Characterization of long and stable de novo single alpha-helix domains provides novel insight into their stability. PMID:28287151
Cytoplasmic Relocalization of TAR DNA-Binding Protein 43 Is Not Sufficient to Reproduce Cellular Pathologies Associated with ALS In vitro. PMID:28286471
Rapid assessment of oxidation via middle-down LCMS correlates with methionine side-chain solvent-accessible surface area for 121 clinical stage monoclonal antibodies. PMID:28281887
Development of an in vitro Bioassay for Recombinant Human Erythropoietin (rHuEPO) Based on Proliferative Stimulation of an Erythroid Cell Line and Analysis of Sialic Acid Dependent Microheterogeneity: UT-7 Cell Bioassay. PMID:28280963
In silico discovery and in vitro activity of inhibitors against Mycobacterium tuberculosis 7,8-diaminopelargonic acid synthase (Mtb BioA). PMID:28280303
A theoretical study on Zn binding loop mutants instigating destabilization and metal binding loss in human SOD1 protein. PMID:28271284
Accurate model annotation of a near-atomic resolution cryo-EM map. PMID:28270620
Bioinformatic analysis of riboswitch structures uncovers variant classes with altered ligand specificity. PMID:28265071
Correlation of fitness landscapes from three orthologous TIM barrels originates from sequence and structure constraints. PMID:28262665
Reducing Virulence and Biofilm of Pseudomonas aeruginosa by Potential Quorum Sensing Inhibitor Carotenoid: Zeaxanthin. PMID:28255686
The activity of a yeast Family 16 methyltransferase, Efm2, is affected by a conserved tryptophan and its N-terminal region. PMID:28255539
Autocatalytic association of proteins by covalent bond formation: a Bio Molecular Welding toolbox derived from a bacterial adhesin. PMID:28252635
A molecular dynamics simulation study decodes the early stage of the disassembly process abolishing the human SAMHD1 function. PMID:28251415
Insight into the orientational versatility of steroid substrates-a docking and molecular dynamics study of a steroid receptor and steroid monooxygenase. PMID:28251412
Raw diffraction data preservation and reuse: overview, update on practicalities and metadata requirements. PMID:28250944
CADEE: Computer-Aided Directed Evolution of Enzymes. PMID:28250941
The relationship between relative solvent accessible surface area (rASA) and irregular structures in protean segments (ProSs). PMID:28250616
Genome-wide identification and comparative expression analysis of LEA genes in watermelon and melon genomes. PMID:28250580
Dynamic New World: Refining Our View of Protein Structure, Function and Evolution. PMID:28250374
String kernels for protein sequence comparisons: improved fold recognition. PMID:28245816
L1198F Mutation Resensitizes Crizotinib to ALK by Altering the Conformation of Inhibitor and ATP Binding Sites. PMID:28245558
Diastereoselective Synthesis of Spirocyclopropanes under Mild Conditions via Formal [2 + 1] Cycloadditions Using 2,3-Dioxo-4-benzylidene-pyrrolidines. PMID:28241452
Insights from molecular dynamics simulations for computational protein design. PMID:28239489
A three-way approach for protein function classification. PMID:28234929
Understanding the roles of intrinsic disorder in subunits of hemoglobin and the disease process of sickle cell anemia. PMID:28232898
Paradoxes and wonders of intrinsic disorder: Complexity of simplicity. PMID:28232895
Missing strings of residues in protein crystal structures. PMID:28232893
The intrinsic disorder alphabet. III. Dual personality of serine. PMID:28232888
Mycobacterium tuberculosis Prolyl Oligopeptidase Induces In vitro Secretion of Proinflammatory Cytokines by Peritoneal Macrophages. PMID:28223969
Anti-trypanosomal activity of non-peptidic nitrile-based cysteine protease inhibitors. PMID:28222138
NO3- anions can act as Lewis acid in the solid state. PMID:28220788
Structure, kinetic characterization and subcellular localization of the two ribulose 5-phosphate epimerase isoenzymes from Trypanosoma cruzi. PMID:28207833
Interacting networks of resistance, virulence and core machinery genes identified by genome-wide epistasis analysis. PMID:28207813
Proteins analysed as virtual knots. PMID:28205562
Understanding in-line probing experiments by modeling cleavage of nonreactive RNA nucleotides. PMID:28202709
Pharmacoinformatics, Adaptive Evolution, and Elucidation of Six Novel Compounds for Schizophrenia Treatment by Targeting DAOA (G72) Isoforms. PMID:28197415
Cancer Stem Cells Therapeutic Target Database: The First Comprehensive Database for Therapeutic Targets of Cancer Stem Cells. PMID:28191780
Combined Docking with Classical Force Field and Quantum Chemical Semiempirical Method PM7. PMID:28191015
OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive. PMID:28190782
Structural and dynamic characterization of a freestanding acyl carrier protein involved in the biosynthesis of cyclic lipopeptide antibiotics. PMID:28187530
SEPIa, a knowledge-driven algorithm for predicting conformational B-cell epitopes from the amino acid sequence. PMID:28183272
Decoding Corticotropin-Releasing Factor Receptor Type 1 Crystal Structures. PMID:28183242
Molecular modeling and molecular dynamic simulation of the effects of variants in the TGFBR2 kinase domain as a paradigm for interpretation of variants obtained by next generation sequencing. PMID:28182693
Structural, mechanistic and functional insight into gliotoxin bis-thiomethylation in Aspergillus fumigatus. PMID:28179499
An editor for the generation and customization of geometry restraints. PMID:28177308
A rapid method for selecting suitable animal species for studying pathogen interactions with plasma protein ligands in vivo. PMID:28168836
The Carboxy Terminus of YCF1 Contains a Motif Conserved throughout >500 Myr of Streptophyte Evolution. PMID:28164224
New biochemical insight of conserved water molecules at catalytic and structural Zn2+ ions in human matrix metalloproteinase-I: a study by MD-simulation. PMID:28161785
ATLAS: A database linking binding affinities with structures for wild-type and mutant TCR-pMHC complexes. PMID:28160322
Theoretical analysis of somatostatin receptor 5 with antagonists and agonists for the treatment of neuroendocrine tumors. PMID:28155055
Modifications of the chromophore of Spinach aptamer based on QM:MM calculations. PMID:28154983
Classifying kinase conformations using a machine learning approach. PMID:28152981
Discovery of Nicotinamide Adenine Dinucleotide Binding Proteins in the Escherichia coli Proteome Using a Combined Energetic- and Structural-Bioinformatics-Based Approach. PMID:28152599
Novel 11β-hydroxysteroid dehydrogenase 1 inhibitors reduce cortisol levels in keratinocytes and improve dermal collagen content in human ex vivo skin after exposure to cortisone and UV. PMID:28152550
Protein Bioinformatics Databases and Resources. PMID:28150231
Binding of small molecules at interface of protein-protein complex - A newer approach to rational drug design. PMID:28149177
Prediction of kinase-inhibitor binding affinity using energetic parameters. PMID:28149052
Dynamics of IRES-mediated translation. PMID:28138065
Exploring the dark foldable proteome by considering hydrophobic amino acids topology. PMID:28134276
The young person's guide to the PDB. PMID:28132477
DRNApred, fast sequence-based method that accurately predicts and discriminates DNA- and RNA-binding residues. PMID:28132027
Calpain-14 and its association with eosinophilic esophagitis. PMID:28131390
The Protein Structure Context of PolyQ Regions. PMID:28125688
3D-e-Chem-VM: Structural Cheminformatics Research Infrastructure in a Freely Available Virtual Machine. PMID:28125221
Identification of a Ligand-Binding Site on the Staphylococcus aureus DnaG Primase C-Terminal Domain. PMID:28125218
High Resolution X-ray Diffraction Dataset for Bacillus licheniformis Gamma Glutamyl Transpeptidase-acivicin complex: SUMO-Tag Renders High Expression and Solubility. PMID:28120227
Utilization of Molecular Dynamics Simulation Coupled with Experimental Assays to Optimize Biocompatibility of an Electrospun PCL/PVA Scaffold. PMID:28118371
Rules of co-occurring mutations characterize the antigenic evolution of human influenza A/H3N2, A/H1N1 and B viruses. PMID:28117657
3D clusters of somatic mutations in cancer reveal numerous rare mutations as functional targets. PMID:28115009
Experimental and In-Silico Investigation of Anti-Microbial Activity of 1-Chloro-2-Isocyanatoethane Derivatives of Thiomorpholine, Piperazine and Morpholine. PMID:28107379
Naphthalimides Selectively Inhibit the Activity of Bacterial, Replicative DNA Ligases and Display Bactericidal Effects against Tubercle Bacilli. PMID:28106753
Insights from the docked DoxDA Model with Thiosulphate. PMID:28104963
RNAHelix: computational modeling of nucleic acid structures with Watson-Crick and non-canonical base pairs. PMID:28102461
Extreme biophysics: Enzymes under pressure. PMID:28101963
Through scaffold modification to 3,5-diaryl-4,5-dihydroisoxazoles: new potent and selective inhibitors of monoamine oxidase B. PMID:28097874
Computational Analysis of Residue Interaction Networks and Coevolutionary Relationships in the Hsp70 Chaperones: A Community-Hopping Model of Allosteric Regulation and Communication. PMID:28095400
Mutation effects predicted from sequence co-variation. PMID:28092658
Non-interacting proteins may resemble interacting proteins: prevalence and implications. PMID:28084410
Structure alignment-based classification of RNA-binding pockets reveals regional RNA recognition motifs on protein surfaces. PMID:28077065
Exploring the stability of ligand binding modes to proteins by molecular dynamics simulations. PMID:28074360
O-GlcNAcylation of STAT5 controls tyrosine phosphorylation and oncogenic transcription in STAT5-dependent malignancies. PMID:28074064
Identification of potential glutaminyl cyclase inhibitors from lead-like libraries by in silico and in vitro fragment-based screening. PMID:28070724
Chimeric influenza haemagglutinins: Generation and use in pseudotype neutralization assays. PMID:28070500
Characterization of BRPMBL, the Bleomycin Resistance Protein Associated with the Carbapenemase NDM. PMID:28069656
Fusing Docking Scoring Functions Improves the Virtual Screening Performance for Discovering Parkinson's Disease Dual Target Ligands. PMID:28067172
In Silico Study of Alkaloids as α-Glucosidase Inhibitors: Hope for the Discovery of Effective Lead Compounds. PMID:28066324
Accuracy comparison of several common implicit solvent models and their implementations in the context of protein-ligand binding. PMID:28064081
Structure-Based Understanding of Binding Affinity and Mode of Estrogen Receptor α Agonists and Antagonists. PMID:28061508
KinMap: a web-based tool for interactive navigation through human kinome data. PMID:28056780
Topological transformations in proteins: effects of heating and proximity of an interface. PMID:28051124
The Role of BAR Domain Proteins in the Regulation of Membrane Dynamics. PMID:28050267
Highly Coarse-Grained Representations of Transmembrane Proteins. PMID:28043122
Sixty-five years of the long march in protein secondary structure prediction: the final stretch? PMID:28040746
Non-Coding RNAs in Lung Cancer: Contribution of Bioinformatics Analysis to the Development of Non-Invasive Diagnostic Tools. PMID:28035947
AnglerFish: a webserver for defining the geometry of α-helices in membrane proteins. PMID:28035031
Burkholderia pseudomallei type III secreted protein BipC: role in actin modulation and translocation activities required for the bacterial intracellular lifecycle. PMID:28028452
CHARMM Force Field Parameterization of Peroxisome Proliferator-Activated Receptor γ Ligands. PMID:28025495
HEDD: the human epigenetic drug database. PMID:28025347
Relative Binding Free Energy Calculations Applied to Protein Homology Models. PMID:28024402
Suppression and synthetic-lethal genetic relationships of ΔgpsB mutations indicate that GpsB mediates protein phosphorylation and penicillin-binding protein interactions in Streptococcus pneumoniae D39. PMID:28010038
FlexPepDock lessons from CAPRI peptide-protein rounds and suggested new criteria for assessment of model quality and utility. PMID:28002624
Simple Physics-Based Analytical Formulas for the Potentials of Mean Force of the Interaction of Amino Acid Side Chains in Water. VII. Charged-Hydrophobic/Polar and Polar-Hydrophobic/Polar Side Chains. PMID:28000446
Aromatic-Aromatic Interactions Enable α-Helix to β-Sheet Transition of Peptides to Form Supramolecular Hydrogels. PMID:27997165
Complex structure of cytochrome c-cytochrome c oxidase reveals a novel protein-protein interaction mode. PMID:27979921
COUSCOus: improved protein contact prediction using an empirical Bayes covariance estimator. PMID:27978812
Rapid Chagas Disease Drug Target Discovery Using Directed Evolution in Drug-Sensitive Yeast. PMID:27977118
Protein S-Bacillithiolation Functions in Thiol Protection and Redox Regulation of the Glyceraldehyde-3-Phosphate Dehydrogenase Gap in Staphylococcus aureus Under Hypochlorite Stress. PMID:27967218
Involvement of Brd4 in different steps of the papillomavirus life cycle. PMID:27965149
Evolutionary and Functional Diversification of the Vitamin D Receptor-Lithocholic Acid Partnership. PMID:27942020
Proteome-Scale Investigation of Protein Allosteric Regulation Perturbed by Somatic Mutations in 7,000 Cancer Genomes. PMID:27939638
Rational screening of peroxisome proliferator-activated receptor-γ agonists from natural products: potential therapeutics for heart failure. PMID:27937122
Discovery of Mycobacterium tuberculosis InhA Inhibitors by Binding Sites Comparison and Ligands Prediction. PMID:27936766
CHARMM-GUI MDFF/xMDFF Utilizer for Molecular Dynamics Flexible Fitting Simulations in Various Environments. PMID:27936734
The evolution of function within the Nudix homology clan. PMID:27936487
Sinu virus, a novel and divergent orthomyxovirus related to members of the genus Thogotovirus isolated from mosquitoes in Colombia. PMID:27936462
Structural basis for glutathione-mediated activation of the virulence regulatory protein PrfA in Listeria. PMID:27930316
In silico studies for the interaction of tumor necrosis factor-alpha (TNF-α) with different saponins from Vietnamese ginseng (Panax vietnamesis). PMID:27924272
Effects of the difference in similarity measures on the comparison of ligand-binding pockets using a reduced vector representation of pockets. PMID:27924268
Conformational shift in the closed state of GroEL induced by ATP-binding triggers a transition to the open state. PMID:27924266
Dynamic profile analysis to characterize dynamics-driven allosteric sites in enzymes. PMID:27924265
TSTMP: target selection for structural genomics of human transmembrane proteins. PMID:27924015
ConEVA: a toolbox for comprehensive assessment of protein contacts. PMID:27923350
Dataset of eye disease-related proteins analyzed using the unfolding mutation screen. PMID:27922631
Piecemeal Buildup of the Genetic Code, Ribosomes, and Genomes from Primordial tRNA Building Blocks. PMID:27918435
A closer look into the α-helix basin. PMID:27917894
Multivalent contacts of the Hsp70 Ssb contribute to its architecture on ribosomes and nascent chain interaction. PMID:27917864
SCOPe: Manual Curation and Artifact Removal in the Structural Classification of Proteins - extended Database. PMID:27914894
mutLBSgeneDB: mutated ligand binding site gene DataBase. PMID:27907895
Crystal Structure of Chitinase ChiW from Paenibacillus sp. str. FPU-7 Reveals a Novel Type of Bacterial Cell-Surface-Expressed Multi-Modular Enzyme Machinery. PMID:27907169
In silico Mapping of Protein Unfolding Mutations for Inherited Disease. PMID:27905547
The SWISS-MODEL Repository-new features and functionality. PMID:27899672
DisProt 7.0: a major update of the database of disordered proteins. PMID:27899601
Identification of a Novel Inhibitory Allosteric Site in p38α. PMID:27898710
Regulation of Gonad Morphogenesis in Drosophila melanogaster by BTB Family Transcription Factors. PMID:27898696
Combating Ebola with Repurposed Therapeutics Using the CANDO Platform. PMID:27898018
Screening of mutations affecting protein stability and dynamics of FGFR1-A simulation analysis. PMID:27896051
AutoDock-GIST: Incorporating Thermodynamics of Active-Site Water into Scoring Function for Accurate Protein-Ligand Docking. PMID:27886114
Identification of Hot Spots in Protein Structures Using Gaussian Network Model and Gaussian Naive Bayes. PMID:27882325
Bioinformatic Identification of Rare Codon Clusters (RCCs) in HBV Genome and Evaluation of RCCs in Proteins Structure of Hepatitis B Virus. PMID:27882067
Structural insights into Gemin5-guided selection of pre-snRNAs for snRNP assembly. PMID:27881600
Rice Cellulose SynthaseA8 Plant-Conserved Region Is a Coiled-Coil at the Catalytic Core Entrance. PMID:27879387
In Silico Exploration for Novel Type-I Inhibitors of Tie-2/TEK: The Performance of Different Selection Strategy in Selecting Virtual Screening Candidates. PMID:27876862
Design, Synthesis, and Evaluation of Dasatinib-Amino Acid and Dasatinib-Fatty Acid Conjugates as Protein Tyrosine Kinase Inhibitors. PMID:27875633
A comparison of the innate flexibilities of six chains in F1-ATPase with identical secondary and tertiary folds; 3 active enzymes and 3 structural proteins. PMID:27872875
Similar compounds versus similar conformers: complementarity between PubChem 2-D and 3-D neighboring sets. PMID:27872662
Molecular Docking Optimization in the Context of Multi-Drug Resistant and Sensitive EGFR Mutants. PMID:27869781
Three-Dimensional Biologically Relevant Spectrum (BRS-3D): Shape Similarity Profile Based on PDB Ligands as Molecular Descriptors. PMID:27869685
De-novo protein function prediction using DNA binding and RNA binding proteins as a test case. PMID:27869118
On the importance of composite protein multiple ligand interactions in protein pockets. PMID:27864975
CHARMM-GUI 10 years for biomolecular modeling and simulation. PMID:27862047
Exploring Molecular Mechanisms of Paradoxical Activation in the BRAF Kinase Dimers: Atomistic Simulations of Conformational Dynamics and Modeling of Allosteric Communication Networks and Signaling Pathways. PMID:27861609
Stereoscopic viewing system for proteins using OpenRasmol: a tool for displaying a filament of proteins. PMID:27857567
The role of charged surface residues in the binding ability of small hubs in protein-protein interaction networks. PMID:27857564
Possible roles of S···O and S···N interactions in the functions and evolution of phospholipase A2. PMID:27857557
Observation selection bias in contact prediction and its implications for structural bioinformatics. PMID:27857150
Identification and Characterization of a New Protein Isoform of Human 5-Lipoxygenase. PMID:27855198
Amyloid-β Peptide Nitrotyrosination Stabilizes Oligomers and Enhances NMDAR-Mediated Toxicity. PMID:27852777
GEN3VA: aggregation and analysis of gene expression signatures from related studies. PMID:27846806
What makes proteins work: exploring life in P-T-X. PMID:27845917
Quantifying side-chain conformational variations in protein structure. PMID:27845406
In silico structural analysis of quorum sensing genes inVibriofischeri. PMID:27844003
Screening and characterization of novel specific peptides targeting MDA-MB-231 claudin-low breast carcinoma by computer-aided phage display methodologies. PMID:27842517
Selenourea: a convenient phasing vehicle for macromolecular X-ray crystal structures. PMID:27841370
Systems pharmacology exploration of botanic drug pairs reveals the mechanism for treating different diseases. PMID:27841365
Intrinsic disorder in proteins involved in amyotrophic lateral sclerosis. PMID:27838743
Empowering pharmacoinformatics by linked life science data. PMID:27830428
Mutation near the binding interfaces at α-hemoglobin stabilizing protein is highly pathogenic. PMID:27830006
Beyond DNA: An Integrated and Functional Approach for Classifying Germline Variants in Breast Cancer Genes. PMID:27822389
MECR Mutations Cause Childhood-Onset Dystonia and Optic Atrophy, a Mitochondrial Fatty Acid Synthesis Disorder. PMID:27817865
Immunoinformatics Approach in Designing Epitope-based Vaccine Against Meningitis-inducing Bacteria (Streptococcus pneumoniae, Neisseria meningitidis, and Haemophilus influenzae Type b). PMID:27812281
The Diversity of Yellow-Related Proteins in Sand Flies (Diptera: Psychodidae). PMID:27812196
Chemogenomics knowledgebase and systems pharmacology for hallucinogen target identification-Salvinorin A as a case study. PMID:27810775
Exploring Human Diseases and Biological Mechanisms by Protein Structure Prediction and Modeling. PMID:27807743
Basis of Protein Stabilization by K Glutamate: Unfavorable Interactions with Carbon, Oxygen Groups. PMID:27806267
DPDR-CPI, a server that predicts Drug Positioning and Drug Repositioning via Chemical-Protein Interactome. PMID:27805045
Computer-aided drug discovery research at a global contract research organization. PMID:27804014
Use of restrained molecular dynamics to predict the conformations of phosphorylated receiver domains in two-component signaling systems. PMID:27802580
The NMR solution structure and function of RPA3313: a putative ribosomal transport protein from Rhodopseudomonas palustris. PMID:27802574
The genomic landscape of core-binding factor acute myeloid leukemias. PMID:27798625
Avoiding Regions Symptomatic of Conformational and Functional Flexibility to Identify Antiviral Targets in Current and Future Coronaviruses. PMID:27797946
S2'-subsite variations between human and mouse enzymes (plasmin, factor XIa, kallikrein) elucidate inhibition differences by tissue factor pathway inhibitor -2 domain1-wild-type, Leu17Arg-mutant and aprotinin. PMID:27797450
Protein Folding and Structure Prediction from the Ground Up II: AAWSEM for α/β Proteins. PMID:27797194
Computational modelling of the binding of arachidonic acid to the human monooxygenase CYP2J2. PMID:27796781
Disposal of iron by a mutant form of lipocalin 2. PMID:27796299
Application of the phase extension method in virus crystallography. PMID:27795615
The RCSB protein data bank: integrative view of protein, gene and 3D structural information. PMID:27794042
Integrated Computational Approach for Virtual Hit Identification against Ebola Viral Proteins VP35 and VP40. PMID:27792169
Predicting Protein-Protein Interaction Sites Using Sequence Descriptors and Site Propensity of Neighboring Amino Acids. PMID:27792167
An integrated 3-Dimensional Genome Modeling Engine for data-driven simulation of spatial genome organization. PMID:27789526
In Silico Prediction of Linear B-Cell Epitopes on Proteins. PMID:27787831
Sequence-Based Prediction of RNA-Binding Residues in Proteins. PMID:27787829
Seeking for Non-Zinc-Binding MMP-2 Inhibitors: Synthesis, Biological Evaluation and Molecular Modelling Studies. PMID:27782083
20(S)-Protopanaxadiol Phospholipid Complex: Process Optimization, Characterization, In Vitro Dissolution and Molecular Docking Studies. PMID:27775578
Mapping the genomic diversity of HCV subtypes 1a and 1b: Implications of structural and immunological constraints for vaccine and drug development. PMID:27774307
Determination of antigenicity-altering patches on the major surface protein of human influenza A/H3N2 viruses. PMID:27774294
Investigating the effects of point mutations on the affinity between the cyanobacterial lectin microvirin and high mannose-type glycans present on the HIV envelope glycoprotein. PMID:27771810
ClusPro-DC: Dimer Classification by the Cluspro Server for Protein-Protein Docking. PMID:27771482
A computational interactome and functional annotation for the human proteome. PMID:27770567
Isatin thiazoline hybrids as dual inhibitors of HIV-1 reverse transcriptase. PMID:27766892
Structural Dynamics Investigation of Human Family 1 & 2 Cystatin-Cathepsin L1 Interaction: A Comparison of Binding Modes. PMID:27764212
Structural Interface Forms and Their Involvement in Stabilization of Multidomain Proteins or Protein Complexes. PMID:27763556
Convert your favorite protein modeling program into a mutation predictor: "MODICT". PMID:27760515
Modeling the Role of Epitope Arrangement on Antibody Binding Stoichiometry in Flaviviruses. PMID:27760352
Accurate Classification of RNA Structures Using Topological Fingerprints. PMID:27755571
Coumarin Antifungal Lead Compounds from Millettia thonningii and Their Predicted Mechanism of Action. PMID:27754464
Antioxidant Activity during Tumor Progression: A Necessity for the Survival of Cancer Cells? PMID:27754368
Broad epitope coverage of a human in vitro antibody library. PMID:27748644
Exploring the Levinthal limit in protein folding. PMID:27743150
A Novel Class of Small Molecule Agonists with Preference for Human over Mouse TLR4 Activation. PMID:27736941
The contribution of major histocompatibility complex contacts to the affinity and kinetics of T cell receptor binding. PMID:27734930
KinView: a visual comparative sequence analysis tool for integrated kinome research. PMID:27731453
Significant Differences in Physicochemical Properties of Human Immunoglobulin Kappa and Lambda CDR3 Regions. PMID:27729912
A Naturally Occurring Antibody Fragment Neutralizes Infectivity of Diverse Infectious Agents. PMID:27725769
Mapping the Geometric Evolution of Protein Folding Motor. PMID:27716851
Simulating cryo electron tomograms of crowded cell cytoplasm for assessment of automated particle picking. PMID:27716029
A method for predicting individual residue contributions to enzyme specificity and binding-site energies, and its application to MTH1. PMID:27714533
Computational prediction shines light on type III secretion origins. PMID:27713481
Cross-Validation of Data Compatibility Between Small Angle X-ray Scattering and Cryo-Electron Microscopy. PMID:27710115
Docking-undocking combination applied to the D3R Grand Challenge 2015. PMID:27709317
An efficient algorithm for protein structure comparison using elastic shape analysis. PMID:27708689
Structural basis for PPAR partial or full activation revealed by a novel ligand binding mode. PMID:27708429
GlycoMinestruct: a new bioinformatics tool for highly accurate mapping of the human N-linked and O-linked glycoproteomes by incorporating structural features. PMID:27708373
Elucidation of the biosynthesis of carnosic acid and its reconstitution in yeast. PMID:27703160
Impact of point mutation P29S in RAC1 on tumorigenesis. PMID:27699663
Molecular docking performance evaluated on the D3R Grand Challenge 2015 drug-like ligand datasets. PMID:27699554
Prediction of phosphothreonine sites in human proteins by fusing different features. PMID:27698459
Improved insights into protein thermal stability: from the molecular to the structurome scale. PMID:27698032
Proteome-wide Structural Analysis of PTM Hotspots Reveals Regulatory Elements Predicted to Impact Biological Function and Disease. PMID:27697855
Distinct roles of immunoreceptor tyrosine-based motifs in immunosuppressive indoleamine 2,3-dioxygenase 1. PMID:27696702
Cofactors-loaded quaternary structure of lysine-specific demethylase 5C (KDM5C) protein: Computational model. PMID:27696497
Effects of point mutations on the thermostability of B. subtilis lipase: investigating nonadditivity. PMID:27696241
Synthesis, Pharmacological Profile and Docking Studies of New Sulfonamides Designed as Phosphodiesterase-4 Inhibitors. PMID:27695125
Increased burden of ultra-rare protein-altering variants among 4,877 individuals with schizophrenia. PMID:27694994
3DFlu: database of sequence and structural variability of the influenza hemagglutinin at population scale. PMID:27694207
Glycyrrhizic Acid Reduces Heart Rate and Blood Pressure by a Dual Mechanism. PMID:27689971
In silico frameworks for systematic pre-clinical screening of potential anti-leukemia therapeutics. PMID:27689915
ProtNN: fast and accurate protein 3D-structure classification in structural and topological space. PMID:27688811
Synthesis and evaluation of C9 alkoxy analogues of (-)-stepholidine as dopamine receptor ligands. PMID:27688181
Insights into the Utility of the Focal Adhesion Scaffolding Proteins in the Anaerobic Fungus Orpinomyces sp. C1A. PMID:27685796
Acidic Residues Control the Dimerization of the N-terminal Domain of Black Widow Spiders' Major Ampullate Spidroin 1. PMID:27681031
To Unveil the Molecular Mechanisms of Qi and Blood through Systems Biology-Based Investigation into Si-Jun-Zi-Tang and Si-Wu-Tang formulae. PMID:27677604
Irreversible inhibitors of the 3C protease of Coxsackie virus through templated assembly of protein-binding fragments. PMID:27677239
Development of a motif-based topology-independent structure comparison method to identify evolutionarily related folds. PMID:27671894
Evolution of Protein Domain Repeats in Metazoa. PMID:27671125
Crystal structure of nonphosphorylated receiver domain of the stress response regulator RcsB from Escherichia coli. PMID:27670836
Utility of a Phylogenetic Perspective in Structural Analysis of CYP72A Enzymes from Flowering Plants. PMID:27669508
Identification of Protein-Protein Interactions via a Novel Matrix-Based Sequence Representation Model with Amino Acid Contact Information. PMID:27669239
Discovery, Molecular Mechanisms, and Industrial Applications of Cold-Active Enzymes. PMID:27667987
Type I interferon causes thrombotic microangiopathy by a dose-dependent toxic effect on the microvasculature. PMID:27663672
Enhancing Virtual Screening Performance of Protein Kinases with Molecular Dynamics Simulations. PMID:27662181
Structured States of Disordered Proteins from Genomic Sequences. PMID:27662088
Evolutionary conservation of Ebola virus proteins predicts important functions at residue level. PMID:27659453
Protein-DNA interfaces: a molecular dynamics analysis of time-dependent recognition processes for three transcription factors. PMID:27658967
Strain analysis of protein structures and low dimensionality of mechanical allosteric couplings. PMID:27655887
Predicting bioactive conformations and binding modes of macrocycles. PMID:27655412
A novel de novo TBX5 mutation in a patient with Holt-Oram syndrome leading to a dramatically reduced biological function. PMID:27652283
PDB2CD: a web-based application for the generation of circular dichroism spectra from protein atomic coordinates. PMID:27651482
Genome-wide survey and phylogeny of S-Ribosylhomocysteinase (LuxS) enzyme in bacterial genomes. PMID:27650568
Identification of 2-oxohistidine Interacting Proteins Using E. coli Proteome Chips. PMID:27644758
Fully Blind Docking at the Atomic Level for Protein-Peptide Complex Structure Prediction. PMID:27642160
DockBench as docking selector tool: the lesson learned from D3R Grand Challenge 2015. PMID:27638810
Analysis of genotype diversity and evolution of Dengue virus serotype 2 using complete genomes. PMID:27635316
Topology independent comparison of RNA 3D structures using the CLICK algorithm. PMID:27634929
dMM-PBSA: A New HADDOCK Scoring Function for Protein-Peptide Docking. PMID:27630991
DAMMIF, a program for rapid ab-initio shape determination in small-angle scattering. PMID:27630371
The role of small in-frame insertions/deletions in inherited eye disorders and how structural modelling can help estimate their pathogenicity. PMID:27628848
Origin of a folded repeat protein from an intrinsically disordered ancestor. PMID:27623012
Combination of In Silico Methods in the Search for Potential CD4(+) and CD8(+) T Cell Epitopes in the Proteome of Leishmania braziliensis. PMID:27621732
Improving the performance of the PLB index for ligand-binding site prediction using dihedral angles and the solvent-accessible surface area. PMID:27619067
An Atomistic View of Amyloidogenic Self-assembly: Structure and Dynamics of Heterogeneous Conformational States in the Pre-nucleation Phase. PMID:27616019
Evolving serodiagnostics by rationally designed peptide arrays: the Burkholderia paradigm in Cystic Fibrosis. PMID:27615705
Essential functions linked with structural disorder in organisms of minimal genome. PMID:27608806
Cation Interactions and Membrane Potential Induce Conformational Changes in NaPi-IIb. PMID:27602725
Deep targeted sequencing in pediatric acute lymphoblastic leukemia unveils distinct mutational patterns between genetic subtypes and novel relapse-associated genes. PMID:27590521
Role of the Conserved Disulfide Bridge in Class A Carbapenemases. PMID:27590339
A theoretical study on predicted protein targets of apple polyphenols and possible mechanisms of chemoprevention in colorectal cancer. PMID:27587238
Design of Heteronuclear Metalloenzymes. PMID:27586347
Substrate prediction of Ixodes ricinus salivary lipocalins differentially expressed during Borrelia afzelii infection. PMID:27584086
dRHP-PseRA: detecting remote homology proteins using profile-based pseudo protein sequence and rank aggregation. PMID:27581095
Tma108, a putative M1 aminopeptidase, is a specific nascent chain-associated protein in Saccharomyces cerevisiae. PMID:27580715
CryGetter: a tool to automate retrieval and analysis of Cry protein data. PMID:27578522
In silico studies of the interaction between BRN2 protein and MORE DNA. PMID:27568376
TMSEG: Novel prediction of transmembrane helices. PMID:27566436
G23D: Online tool for mapping and visualization of genomic variants on 3D protein structures. PMID:27565432
Regulation of Polycystin-1 Function by Calmodulin Binding. PMID:27560828
Prediction of Protein Structure Using Surface Accessibility Data. PMID:27560616
KScons: a Bayesian approach for protein residue contact prediction using the knob-socket model of protein tertiary structure. PMID:27559156
Genome-wide identification of salinity responsive HSP70s in common bean. PMID:27558093
Large-Scale Recombinant Expression and Purification of Human Tyrosinase Suitable for Structural Studies. PMID:27551823
Lincosamides, Streptogramins, Phenicols, and Pleuromutilins: Mode of Action and Mechanisms of Resistance. PMID:27549310
Electrostatic component of binding energy: Interpreting predictions from poisson-boltzmann equation and modeling protocols. PMID:27546093
Electrostatic component of binding energy: Interpreting predictions from poisson-boltzmann equation and modeling protocols. PMID:27546093
Docking Studies and Molecular Dynamic Simulations Reveal Different Features of IDO1 Structure. PMID:27546049
Discovery and synthetic optimization of a novel scaffold for hydrophobic tunnel-targeted autotaxin inhibition. PMID:27544588
Lupus high-density lipoprotein induces proinflammatory responses in macrophages by binding lectin-like oxidised low-density lipoprotein receptor 1 and failing to promote activating transcription factor 3 activity. PMID:27543414
The Hexahistidine Motif of Host-Defense Protein Human Calprotectin Contributes to Zinc Withholding and Its Functional Versatility. PMID:27541598
A preliminary review of influential works in data-driven discovery. PMID:27540499
Xanthine dehydrogenase: An old enzyme with new knowledge and prospects. PMID:27537049
Discovery of peptide inhibitors targeting human programmed death 1 (PD-1) receptor. PMID:27533458
Benzene Probes in Molecular Dynamics Simulations Reveal Novel Binding Sites for Ligand Design. PMID:27532490
Positive Selection Pressure Drives Variation on the Surface-Exposed Variable Proteins of the Pathogenic Neisseria. PMID:27532335
Sorting protein decoys by machine-learning-to-rank. PMID:27530967
Carboxylic ester hydrolases: Classification and database derived from their primary, secondary, and tertiary structures. PMID:27530203
HLA-B*51:01 is strongly associated with clindamycin-related cutaneous adverse drug reactions. PMID:27527109
Understanding the molecular basis of substrate binding specificity of PTB domains. PMID:27526776
Diverse activation pathways in class A GPCRs converge near the G-protein-coupling region. PMID:27525504
Conformation-dependent restraints for polynucleotides: I. Clustering of the geometry of the phosphodiester group. PMID:27521371
Paralog-Specific Patterns of Structural Disorder and Phosphorylation in the Vertebrate SH3-SH2-Tyrosine Kinase Protein Family. PMID:27519537
A Systematic Analysis of the Structures of Heterologously Expressed Proteins and Those from Their Native Hosts in the RCSB PDB Archive. PMID:27517583
Antigenic characterization of classical swine fever virus YC11WB isolates from wild boar. PMID:27515269
Extensively Parameterized Mutation-Selection Models Reliably Capture Site-Specific Selective Constraint. PMID:27512115
A novel secondary structure based on fused five-membered rings motif. PMID:27511362
MMpI: A WideRange of Available Compounds of Matrix Metalloproteinase Inhibitors. PMID:27509041
Data on publications, structural analyses, and queries used to build and utilize the AlloRep database. PMID:27508249
IPMiner: hidden ncRNA-protein interaction sequential pattern mining with stacked autoencoder for accurate computational prediction. PMID:27506469
Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. PMID:27504778
An in silico algorithm for identifying stabilizing pockets in proteins: test case, the Y220C mutant of the p53 tumor suppressor protein. PMID:27503952
Membrane Proteins Are Dramatically Less Conserved than Water-Soluble Proteins across the Tree of Life. PMID:27501943
PL-PatchSurfer2: Improved Local Surface Matching-Based Virtual Screening Method That Is Tolerant to Target and Ligand Structure Variation. PMID:27500657
Macromolecular Crystallography and Structural Biology Databases at NIST. PMID:27500071
Microscopic Characterization of Membrane Transporter Function by In Silico Modeling and Simulation. PMID:27497175
Continuum Electrostatics Approaches to Calculating pKas and Ems in Proteins. PMID:27497160
Single Agent and Synergistic Activity of the "First-in-Class" Dual PI3K/BRD4 Inhibitor SF1126 with Sorafenib in Hepatocellular Carcinoma. PMID:27496136
Comprehensive analysis of the Co-structures of dipeptidyl peptidase IV and its inhibitor. PMID:27491540
Adaptive local learning in sampling based motion planning for protein folding. PMID:27490494
Driving Structure-Based Drug Discovery through Cosolvent Molecular Dynamics. PMID:27486927
Identification of Multiple Cryptococcal Fungicidal Drug Targets by Combined Gene Dosing and Drug Affinity Responsive Target Stability Screening. PMID:27486194
From ZikV genome to vaccine: in silico approach for the epitope-based peptide vaccine against Zika virus envelope glycoprotein. PMID:27485738
Human Naa50 Protein Displays Broad Substrate Specificity for Amino-terminal Acetylation: DETAILED STRUCTURAL AND BIOCHEMICAL ANALYSIS USING TETRAPEPTIDE LIBRARY. PMID:27484799
Prospective evaluation of shape similarity based pose prediction method in D3R Grand Challenge 2015. PMID:27484214
Docking pose selection by interaction pattern graph similarity: application to the D3R grand challenge 2015. PMID:27480696
Genetic variation in MHC proteins is associated with T cell receptor expression biases. PMID:27479906
The trickle before the torrent-diffraction data from X-ray lasers. PMID:27479637
m(1)A and m(1)G disrupt A-RNA structure through the intrinsic instability of Hoogsteen base pairs. PMID:27478929
Binding interaction of a gamma-aminobutyric acid derivative with serum albumin: an insight by fluorescence and molecular modeling analysis. PMID:27478738
PIMADb: A Database of Protein-Protein Interactions in Huge Macromolecular Assemblies. PMID:27478368
A Multi-scale Computational Platform to Mechanistically Assess the Effect of Genetic Variation on Drug Responses in Human Erythrocyte Metabolism. PMID:27467583
Quantifying Nonnative Interactions in the Protein-Folding Free-Energy Landscape. PMID:27463131
Impact of the Recent Mouse P-Glycoprotein Structure for Structure-Based Ligand Design. PMID:27463054
The 3-D Structural Basis for the Pgi Genotypic Differences in the Performance of the Butterfly Melitaea cinxia at Different Temperatures. PMID:27462709
Characterisation of a New Fungal Immunomodulatory Protein from Tiger Milk mushroom, Lignosus rhinocerotis. PMID:27460640
Agroinfiltration contributes to VP1 recombinant protein degradation. PMID:27459147
Comprehensive N-Glycan Profiling of Avian Immunoglobulin Y. PMID:27459092
Getting the most out of PubChem for virtual screening. PMID:27454129
The archiving and dissemination of biological structure data. PMID:27450113
Tracking the Antigenic Evolution of Foot-and-Mouth Disease Virus. PMID:27448206
Exhaustive Conformational Sampling of Complex Fused Ring Macrocycles Using Inverse Kinematics. PMID:27447193
The Crystal Structure of the C-Terminal Domain of the Salmonella enterica PduO Protein: An Old Fold with a New Heme-Binding Mode. PMID:27446048
Therapeutics Insight with Inclusive Immunopharmacology Explication of Human Rotavirus A for the Treatment of Diarrhea. PMID:27445802
Pharmacophore modeling and in silico toxicity assessment of potential anticancer agents from African medicinal plants. PMID:27445461
In-silico discovery of cancer-specific peptide-HLA complexes for targeted therapy. PMID:27439771
Drug search for leishmaniasis: a virtual screening approach by grid computing. PMID:27438595
Origin and Functional Prediction of Pollen Allergens in Plants. PMID:27436829
PreFRP: Prediction and visualization of fluctuation residues in proteins. PMID:27433060
Biophysically inspired model for functionalized nanocarrier adhesion to cell surface: roles of protein expression and mechanical factors. PMID:27429783
In silico approach to explore the disruption in the molecular mechanism of human hyaluronidase 1 by mutant E268K that directs Natowicz syndrome. PMID:27424109
Online interactive analysis of protein structure ensembles with Bio3D-web. PMID:27423893
Chopping and Changing: the Evolution of the Flavin-dependent Monooxygenases. PMID:27423402
Protein function in precision medicine: deep understanding with machine learning. PMID:27423136
GeauxDock: Accelerating Structure-Based Virtual Screening with Heterogeneous Computing. PMID:27420300
Computational Study of the Binding Mechanism of Actin-Depolymerizing Factor 1 with Actin in Arabidopsis thaliana. PMID:27414648
GP0.4 from bacteriophage T7: in silico characterisation of its structure and interaction with E. coli FtsZ. PMID:27411831
Protein Composition Determines the Effect of Crowding on the Properties of Disordered Proteins. PMID:27410731
To Keep or Not to Keep? The Question of Crystallographic Waters for Enzyme Simulations in Organic Solvent. PMID:27403032
Chemical Structure-Biological Activity Models for Pharmacophores' 3D-Interactions. PMID:27399692
Understanding the dynamics of monomeric, dimeric, and tetrameric α-synuclein structures in water. PMID:27398307
Probing Lipophilic Adamantyl Group as the P1-Ligand for HIV-1 Protease Inhibitors: Design, Synthesis, Protein X-ray Structural Studies, and Biological Evaluation. PMID:27389367
HVint: A Strategy for Identifying Novel Protein-Protein Interactions in Herpes Simplex Virus Type 1. PMID:27384951
Sequence-Specific Recognition of DNA by Proteins: Binding Motifs Discovered Using a Novel Statistical/Computational Analysis. PMID:27384774
FastRNABindR: Fast and Accurate Prediction of Protein-RNA Interface Residues. PMID:27383535
Experimental Analysis of Functional Variation within Protein Families: Receiver Domain Autodephosphorylation Kinetics. PMID:27381915
A pose prediction approach based on ligand 3D shape similarity. PMID:27379501
Inter- and Intra-Subunit Butanol/Isoflurane Sites of Action in the Human Glycine Receptor. PMID:27378846
Performance of protein-structure predictions with the physics-based UNRES force field in CASP11. PMID:27378298
Second harmonic generation correlation spectroscopy for characterizing translationally diffusing protein nanocrystals. PMID:27377382
ERK1 and ERK2 Map Kinases: Specific Roles or Functional Redundancy? PMID:27376062
Drug Design for CNS Diseases: Polypharmacological Profiling of Compounds Using Cheminformatic, 3D-QSAR and Virtual Screening Methodologies. PMID:27375423
The X-ray Structures of Six Octameric RNA Duplexes in the Presence of Different Di- and Trivalent Cations. PMID:27355942
Molecular dynamics simulations and structure-based network analysis reveal structural and functional aspects of G-protein coupled receptor dimer interactions. PMID:27349423
Lessons Learned over Four Benchmark Exercises from the Community Structure-Activity Resource. PMID:27345761
Novel drug design for Chagas disease via targeting Trypanosoma cruzi tubulin: Homology modeling and binding pocket prediction on Trypanosoma cruzi tubulin polymerization inhibition by naphthoquinone derivatives. PMID:27345756
HU histone-like DNA-binding protein from Thermus thermophilus: structural and evolutionary analyses. PMID:27342116
Functional Characterization of Soybean Glyma04g39610 as a Brassinosteroid Receptor Gene and Evolutionary Analysis of Soybean Brassinosteroid Receptors. PMID:27338344
Molecular Cloning of HbPR-1 Gene from Rubber Tree, Expression of HbPR-1 Gene in Nicotiana benthamiana and Its Inhibition of Phytophthora palmivora. PMID:27337148
Crystal Structures of the Global Regulator DasR from Streptomyces coelicolor: Implications for the Allosteric Regulation of GntR/HutC Repressors. PMID:27337024
Molecular Evolution of the Oxygen-Binding Hemerythrin Domain. PMID:27336621
Exploring the Membrane Potential of Simple Dual-Membrane Systems as Models for Gap-Junction Channels. PMID:27332126
Structural Elements in the Gαs and Gαq C Termini That Mediate Selective G Protein-coupled Receptor (GPCR) Signaling. PMID:27330078
Redesigning Aldolase Stereoselectivity by Homologous Grafting. PMID:27327271
Geometry of guanidinium groups in arginines. PMID:27326702
Rice bifunctional phytocystatin is a dual modulator of legumain and papain-like proteases. PMID:27325119
ORION: a web server for protein fold recognition and structure prediction using evolutionary hybrid profiles. PMID:27319297
Next-generation sequencing reveals substantial genetic contribution to dementia with Lewy bodies. PMID:27312774
Proteome-wide covalent ligand discovery in native biological systems. PMID:27309814
Structure-based prediction of transcription factor binding specificity using an integrative energy function. PMID:27307632
Finding correct protein-protein docking models using ProQDock. PMID:27307625
Picosecond Photobiology: Watching a Signaling Protein Function in Real Time via Time-Resolved Small- and Wide-Angle X-ray Scattering. PMID:27305463
Characterization of Five Novel Brevibacillus Bacteriophages and Genomic Comparison of Brevibacillus Phages. PMID:27304881
IDAAPM: integrated database of ADMET and adverse effects of predictive modeling based on FDA approved drug data. PMID:27303447
Association of HLA class I and II genes with cutaneous leishmaniasis: a case control study from Sri Lanka and a systematic review. PMID:27301744
Arabinoamidine synthesis and its inhibition toward β-glucosidase (sweet almonds) in comparison to a library of galactonoamidines. PMID:27298003
Protein-structure-guided discovery of functional mutations across 19 cancer types. PMID:27294619
Impacts of Nonsynonymous Single Nucleotide Polymorphisms of Adiponectin Receptor 1 Gene on Corresponding Protein Stability: A Computational Approach. PMID:27294143
Literature information in PubChem: associations between PubChem records and scientific articles. PMID:27293485
PDNAsite: Identification of DNA-binding Site from Protein Sequence by Incorporating Spatial and Sequence Context. PMID:27282833
Mechanism of Histone H3K4me3 Recognition by the Plant Homeodomain of Inhibitor of Growth 3. PMID:27281824
Improved prediction of antibody VL-VH orientation. PMID:27276984
Structural and Functional Characterization of a Novel Family of Cyclophilins, the AquaCyps. PMID:27276069
NMR as a tool to investigate the structure, dynamics and function of membrane proteins. PMID:27273629
On methylene-bridged cysteine and lysine residues in proteins. PMID:27261771
QSAR-Driven Discovery of Novel Chemical Scaffolds Active against Schistosoma mansoni. PMID:27253773
Diffraction Techniques in Structural Biology. PMID:27248784
A Terpene Synthase Is Involved in the Synthesis of the Volatile Organic Compound Sodorifen of Serratia plymuthica 4Rx13. PMID:27242752
Blind Evaluation of Hybrid Protein Structure Analysis Methods based on Cross-Linking. PMID:27242194
Analysis of the interactions of sulfur-containing amino acids in membrane proteins. PMID:27240306
Pharmacoinformatic and molecular docking studies reveal potential novel antidepressants against neurodegenerative disorders by targeting HSPB8. PMID:27226709
Neuron-Like Networks Between Ribosomal Proteins Within the Ribosome. PMID:27225526
Lead identification for the K-Ras protein: virtual screening and combinatorial fragment-based approaches. PMID:27217775
QwikMD - Integrative Molecular Dynamics Toolkit for Novices and Experts. PMID:27216779
Wake me when it's over - Bacterial toxin-antitoxin proteins and induced dormancy. PMID:27216598
Screening dietary flavonoids for the reversal of P-glycoprotein-mediated multidrug resistance in cancer. PMID:27216424
From Binding-Induced Dynamic Effects in SH3 Structures to Evolutionary Conserved Sectors. PMID:27213566
Structural diversity in a human antibody germline library. PMID:27210805
BindUP: a web server for non-homology-based prediction of DNA and RNA binding proteins. PMID:27198220
Dissemination of original NMR data enhances reproducibility and integrity in chemical research. PMID:27197893
Promiscuity in the Enzymatic Catalysis of Phosphate and Sulfate Transfer. PMID:27187273
iPARTS2: an improved tool for pairwise alignment of RNA tertiary structures, version 2. PMID:27185896
Improved Species-Specific Lysine Acetylation Site Prediction Based on a Large Variety of Features Set. PMID:27183223
Visualizing ensembles in structural biology. PMID:27179343
MoRFchibi SYSTEM: software tools for the identification of MoRFs in protein sequences. PMID:27174932
PSSweb: protein structural statistics web server. PMID:27174930
Identification of quinones as novel PIM1 kinase inhibitors. PMID:27173800
Unconventional N-H…N Hydrogen Bonds Involving Proline Backbone Nitrogen in Protein Structures. PMID:27166805
ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules. PMID:27166375
Constructing Structure Ensembles of Intrinsically Disordered Proteins from Chemical Shift Data. PMID:27159632
Addressing the Role of Conformational Diversity in Protein Structure Prediction. PMID:27159429
Effect of Binding Pose and Modeled Structures on SVMGen and GlideScore Enrichment of Chemical Libraries. PMID:27154487
PinSnps: structural and functional analysis of SNPs in the context of protein interaction networks. PMID:27153707
FRAGSION: ultra-fast protein fragment library generation by IOHMM sampling. PMID:27153697
Crystal Structure of Human Herpesvirus 6B Tegument Protein U14. PMID:27152739
Genome-wide investigation and expression analysis of AP2-ERF gene family in salt tolerant common bean. PMID:27152109
Small Molecules Antagonise the MIA-Fibronectin Interaction in Malignant Melanoma. PMID:27151361
FoXS, FoXSDock and MultiFoXS: Single-state and multi-state structural modeling of proteins and their complexes based on SAXS profiles. PMID:27151198
StructMAn: annotation of single-nucleotide polymorphisms in the structural context. PMID:27150811
MutaBind estimates and interprets the effects of sequence variants on protein-protein interactions. PMID:27150810
CSAR 2014: A Benchmark Exercise Using Unpublished Data from Pharma. PMID:27149958
Estimation of Uncertainties in the Global Distance Test (GDT_TS) for CASP Models. PMID:27149620
Protein Folding and Structure Prediction from the Ground Up: The Atomistic Associative Memory, Water Mediated, Structure and Energy Model. PMID:27148634
Statistical analysis of structural determinants for protein-DNA-binding specificity. PMID:27147539
Cations Stiffen Actin Filaments by Adhering a Key Structural Element to Adjacent Subunits. PMID:27146246
Peptiderive server: derive peptide inhibitors from protein-protein interactions. PMID:27141963
Structure of a prereaction complex between the nerve agent sarin, its biological target acetylcholinesterase, and the antidote HI-6. PMID:27140636
Functional Sites Induce Long-Range Evolutionary Constraints in Enzymes. PMID:27138088
Structure elucidation of the Pribnow box consensus promoter sequence by racemic DNA crystallography. PMID:27137886
Pulchrin A, a New Natural Coumarin Derivative of Enicosanthellum pulchrum, Induces Apoptosis in Ovarian Cancer Cells via Intrinsic Pathway. PMID:27136097
Cyclic Ketoximes as Estrogen Receptor β Selective Agonists. PMID:27135651
Characterization of pioglitazone cyclodextrin complexes: Molecular modeling to in vivo evaluation. PMID:27134470
The MPI bioinformatics Toolkit as an integrative platform for advanced protein sequence and structure analysis. PMID:27131380
Structural evidence of the species-dependent albumin binding of the modified cyclic phosphatidic acid with cytotoxic properties. PMID:27129297
PPMP, a novel tubulin-depolymerizing agent against esophageal cancer in patient-derived tumor xenografts. PMID:27129160
Structure of a bd oxidase indicates similar mechanisms for membrane-integrated oxygen reductases. PMID:27126043
Geometric Simulation Approach for Grading and Assessing the Thermostability of CALBs. PMID:27123343
An Electrostatic Funnel in the GABA-Binding Pathway. PMID:27119953
Protein Residue Contacts and Prediction Methods. PMID:27115648
Combined sequence and sequence-structure based methods for analyzing FGF23, CYP24A1 and VDR genes. PMID:27114920
Genetics of PCOS: A systematic bioinformatics approach to unveil the proteins responsible for PCOS. PMID:27114910
Exploring the chemical space of influenza neuraminidase inhibitors. PMID:27114890
Endogenous growth factor stimulation of hemocyte proliferation induces resistance to Schistosoma mansoni challenge in the snail host. PMID:27114544
CoReCG: a comprehensive database of genes associated with colon-rectal cancer. PMID:27114494
From data repositories to submission portals: rethinking the role of domain-specific databases in CollecTF. PMID:27114493
RaptorX-Property: a web server for protein structure property prediction. PMID:27112573
Improvements in GROMACS plugin for PyMOL including implicit solvent simulations and displaying results of PCA analysis. PMID:27107576
Knowledge-Based Methods To Train and Optimize Virtual Screening Ensembles. PMID:27097522
Acyl carrier proteins from sunflower (Helianthus annuus L.) seeds and their influence on FatA and FatB acyl-ACP thioesterase activities. PMID:27095109
Genomic Landscape Survey Identifies SRSF1 as a Key Oncodriver in Small Cell Lung Cancer. PMID:27093186
Pharmacogenomics of Scopoletin in Tumor Cells. PMID:27092478
Geomfinder: a multi-feature identifier of similar three-dimensional protein patterns: a ligand-independent approach. PMID:27092185
Improving Viral Protease Inhibitors to Counter Drug Resistance. PMID:27090931
ProViz-a web-based visualization tool to investigate the functional and evolutionary features of protein sequences. PMID:27085803
RBscore&NBench: a high-level web server for nucleic acid binding residues prediction with a large-scale benchmarking database. PMID:27084939
Crystal Structures of Apo and Liganded 4-Oxalocrotonate Decarboxylase Uncover a Structural Basis for the Metal-Assisted Decarboxylation of a Vinylogous β-Keto Acid. PMID:27082660
Unraveling the Deleterious Effects of Cancer-Driven STK11 Mutants Through Conformational Sampling Approach. PMID:27081308
Crystal Structure of the GRAS Domain of SCARECROW-LIKE7 in Oryza sativa. PMID:27081181
Structural and Affinity Determinants in the Interaction between Alcohol Acyltransferase from F. x ananassa and Several Alcohol Substrates: A Computational Study. PMID:27078149
Removal of the Side Chain at the Active-Site Serine by a Glycine Substitution Increases the Stability of a Wide Range of Serine β-Lactamases by Relieving Steric Strain. PMID:27073009
Comparing pharmacophore models derived from crystal structures and from molecular dynamics simulations. PMID:27069282
XLSearch: a Probabilistic Database Search Algorithm for Identifying Cross-Linked Peptides. PMID:27068484
Identifying Allosteric Hotspots with Dynamics: Application to Inter- and Intra-species Conservation. PMID:27066750
Structural Investigations of N-carbamoylputrescine Amidohydrolase from Medicago truncatula: Insights into the Ultimate Step of Putrescine Biosynthesis in Plants. PMID:27066023
Experimental and Metabolic Modeling Evidence for a Folate-Cleaving Side-Activity of Ketopantoate Hydroxymethyltransferase (PanB). PMID:27065985
FAM46 proteins are novel eukaryotic non-canonical poly(A) polymerases. PMID:27060136
Positioning the Intracellular Salt Potassium Glutamate in the Hofmeister Series by Chemical Unfolding Studies of NTL9. PMID:27054379
The Ascaris suum nicotinic receptor, ACR-16, as a drug target: Four novel negative allosteric modulators from virtual screening. PMID:27054065
Surface energetics and protein-protein interactions: analysis and mechanistic implications. PMID:27050828
The Functional Human C-Terminome. PMID:27050421
Conformational diversity and enantioconvergence in potato epoxide hydrolase 1. PMID:27049844
Efficacy and Toxicity Assessment of Different Antibody Based Antiangiogenic Drugs by Computational Docking Method. PMID:27047544
Molecular Dynamics Simulations to Investigate the Influences of Amino Acid Mutations on Protein Three-Dimensional Structures of Cytochrome P450 2D6.1, 2, 10, 14A, 51, and 62. PMID:27046024
Structure-Based Analysis Reveals Cancer Missense Mutations Target Protein Interaction Interfaces. PMID:27043210
The histone chaperone Vps75 forms multiple oligomeric assemblies capable of mediating exchange between histone H3-H4 tetramers and Asf1-H3-H4 complexes. PMID:27036862
Treating Diabetes Mellitus: Pharmacophore Based Designing of Potential Drugs from Gymnema sylvestre against Insulin Receptor Protein. PMID:27034931
Gene Prioritization by Integrated Analysis of Protein Structural and Network Topological Properties for the Protein-Protein Interaction Network of Neurological Disorders. PMID:27034906
In Silico Approach for SAR Analysis of the Predicted Model of DEPDC1B: A Novel Target for Oral Cancer. PMID:27034663
Imbalance in chemical space: How to facilitate the identification of protein-protein interaction inhibitors. PMID:27034268
An optimized single chain TCR scaffold relying on the assembly with the native CD3-complex prevents residual mispairing with endogenous TCRs in human T-cells. PMID:27028870
Utility of the Biosynthetic Folate Pathway for Targets in Antimicrobial Discovery. PMID:27025730
Trimethylamine-N-oxide switches from stabilizing nature: A mechanistic outlook through experimental techniques and molecular dynamics simulation. PMID:27025561
Structure-Based Drug Design of Small Molecule Peptide Deformylase Inhibitors to Treat Cancer. PMID:27023495
CoDNaS 2.0: a comprehensive database of protein conformational diversity in the native state. PMID:27022160
Fast antibody fragment motion: flexible linkers act as entropic spring. PMID:27020739
Anaplasma phagocytophilum increases the levels of histone modifying enzymes to inhibit cell apoptosis and facilitate pathogen infection in the tick vector Ixodes scapularis. PMID:27019326
Molprobity's ultimate rotamer-library distributions for model validation. PMID:27018641
CCProf: exploring conformational change profile of proteins. PMID:27016699
Template-based protein-protein docking exploiting pairwise interfacial residue restraints. PMID:27013645
HNdb: an integrated database of gene and protein information on head and neck squamous cell carcinoma. PMID:27013077
SM-TF: A structural database of small molecule-transcription factor complexes. PMID:27010673
De novo PMP2 mutations in families with type 1 Charcot-Marie-Tooth disease. PMID:27009151
Importance of the Linker Region in Matrix Metalloproteinase-1 Domain Interactions. PMID:26998255
Wikidata as a semantic framework for the Gene Wiki initiative. PMID:26989148
Refinement of atomic models in high resolution EM reconstructions using Flex-EM and local assessment. PMID:26988127
Inhibition of Mycobacterium-RmlA by Molecular Modeling, Dynamics Simulation, and Docking. PMID:26981117
A New Secondary Structure Assignment Algorithm Using Cα Backbone Fragments. PMID:26978354
The FAIR Guiding Principles for scientific data management and stewardship. PMID:26978244
PDP-CON: prediction of domain/linker residues in protein sequences using a consensus approach. PMID:26969678
Modeling of babesipain-1 and identification of natural and synthetic leads for bovine babesiosis drug development. PMID:26969677
Length-independent structural similarities enrich the antibody CDR canonical class model. PMID:26963563
Genome-wide survey of codons under diversifying selection in a highly recombining bacterial species, Helicobacter pylori. PMID:26961370
Synthesis and Larvicidal Activity of Novel Thenoylhydrazide Derivatives. PMID:26960713
Structural and Functional Aspects of Class A Carbapenemases. PMID:26960341
Identification of Toxic Pyrrolizidine Alkaloids and Their Common Hepatotoxicity Mechanism. PMID:26959016
Large scale rigidity-based flexibility analysis of biomolecules. PMID:26958583
Structural insights of a PI3K/mTOR dual inhibitor with the morpholino-triazine scaffold. PMID:26956874
CoeViz: a web-based tool for coevolution analysis of protein residues. PMID:26956673
SNP2Structure: A Public and Versatile Resource for Mapping and Three-Dimensional Modeling of Missense SNPs on Human Protein Structures. PMID:26949480
Mimicking titration experiments with MD simulations: A protocol for the investigation of pH-dependent effects on proteins. PMID:26936826
Using a Genetically Encoded Sensor to Identify Inhibitors of Toxoplasma gondii Ca2+ Signaling. PMID:26933036
The Combining Sites of Anti-lipid A Antibodies Reveal a Widely Utilized Motif Specific for Negatively Charged Groups. PMID:26933033
Delineation of Polypharmacology across the Human Structural Kinome Using a Functional Site Interaction Fingerprint Approach. PMID:26929980
Molecular Docking and Molecular Dynamics to Identify a Novel Human Immunodeficiency Virus Inhibitor from Alkaloids of Toddalia asiatica. PMID:26929575
Robust classification of protein variation using structural modelling and large-scale data integration. PMID:26926108
Prior knowledge or freedom of interpretation? A critical look at a recently published classification of "novel" Zn binding sites. PMID:26914344
Molecular association of glucose-6-phosphate isomerase and pyruvate kinase M2 with glyceraldehyde-3-phosphate dehydrogenase in cancer cells. PMID:26911935
Unique PFK regulatory property from some mosquito vectors of disease, and from Drosophila melanogaster. PMID:26911930
Evolutionary Dynamics of Floral Homeotic Transcription Factor Protein-Protein Interactions. PMID:26908583
In Silico Screening Identifies a Novel Potential PARP1 Inhibitor Targeting Synthetic Lethality in Cancer Treatment. PMID:26907257
Pooled screening for antiproliferative inhibitors of protein-protein interactions. PMID:26900867
Arginine side chain interactions and the role of arginine as a gating charge carrier in voltage sensitive ion channels. PMID:26899474
EDGA: A Population Evolution Direction-Guided Genetic Algorithm for Protein-Ligand Docking. PMID:26895461
Virtual screening of the inhibitors targeting at the viral protein 40 of Ebola virus. PMID:26888469
Integrating TRPV1 Receptor Function with Capsaicin Psychophysics. PMID:26884754
Effect of Ethanol on the Metabolic Characteristics of HIV-1 Integrase Inhibitor Elvitegravir and Elvitegravir/Cobicistat with CYP3A: An Analysis Using a Newly Developed LC-MS/MS Method. PMID:26872388
Crystal structure and functional implications of the tandem-type universal stress protein UspE from Escherichia coli. PMID:26865045
Engineered hapten-binding antibody derivatives for modulation of pharmacokinetic properties of small molecules and targeted payload delivery. PMID:26864111
Electrochemical insights into the mechanism of NiFe membrane-bound hydrogenases. PMID:26862221
Probing the ATP-induced conformational flexibility of the PcrA helicase protein using molecular dynamics simulation. PMID:26860503
Biochemical Methods To Investigate lncRNA and the Influence of lncRNA:Protein Complexes on Chromatin. PMID:26859437
CryptoSite: Expanding the Druggable Proteome by Characterization and Prediction of Cryptic Binding Sites. PMID:26854760
Bridging semantics and syntax with graph algorithms-state-of-the-art of extracting biomedical relations. PMID:26851224
Easy mammalian expression and crystallography of maltose-binding protein-fused human proteins. PMID:26850170
On Nature's Strategy for Assigning Genetic Code Multiplicity. PMID:26849571
Structure-Activity Relationship of Chlorotoxin-Like Peptides. PMID:26848686
mutation3D: Cancer Gene Prediction Through Atomic Clustering of Coding Variants in the Structural Proteome. PMID:26841357
Safeguarding Structural Data Repositories against Bad Apples. PMID:26840827
Self Organizing Map-Based Classification of Cathepsin k and S Inhibitors with Different Selectivity Profiles Using Different Structural Molecular Fingerprints: Design and Application for Discovery of Novel Hits. PMID:26840291
Synthetic Peptides as Protein Mimics. PMID:26835447
On the satisfaction of backbone-carbonyl lone pairs of electrons in protein structures. PMID:26833776
The Chlamydia trachomatis Protease CPAF Contains a Cryptic PDZ-Like Domain with Similarity to Human Cell Polarity and Tight Junction PDZ-Containing Proteins. PMID:26829550
In-Silico Computing of the Most Deleterious nsSNPs in HBA1 Gene. PMID:26824843
Dissecting protein architecture with communication blocks and communicating segment pairs. PMID:26823083
Conformational Dynamics, Ligand Binding and Effects of Mutations in NirE an S-Adenosyl-L-Methionine Dependent Methyltransferase. PMID:26822701
Inhibiting Helicobacter pylori HtrA protease by addressing a computationally predicted allosteric ligand binding site. PMID:26819700
UbiSite: incorporating two-layered machine learning method with substrate motifs to predict ubiquitin-conjugation site on lysines. PMID:26818456
Knowledge-based three-body potential for transcription factor binding site prediction. PMID:26816396
BLAST-based structural annotation of protein residues using Protein Data Bank. PMID:26810894
Selection on protein structure, interaction, and sequence. PMID:26808055
BISQUE: locus- and variant-specific conversion of genomic, transcriptomic and proteomic database identifiers. PMID:26803163
Ribonuclease H/DNA Polymerase HIV-1 Reverse Transcriptase Dual Inhibitor: Mechanistic Studies on the Allosteric Mode of Action of Isatin-Based Compound RMNC6. PMID:26800261
The role of negative selection in protein evolution revealed through the energetics of the native state ensemble. PMID:26800099
Uncovering New Pathogen-Host Protein-Protein Interactions by Pairwise Structure Similarity. PMID:26799490
Role of Bassoon and Piccolo in Assembly and Molecular Organization of the Active Zone. PMID:26793095
CHSalign: A Web Server That Builds upon Junction-Explorer and RNAJAG for Pairwise Alignment of RNA Secondary Structures with Coaxial Helical Stacking. PMID:26789998
Structure of a HOIP/E2~ubiquitin complex reveals RBR E3 ligase mechanism and regulation. PMID:26789245
Natural HCV variants with increased replicative fitness due to NS3 helicase mutations in the C-terminal helix α18. PMID:26787124
Centers of motion associated with EF-Tu binding to the ribosome. PMID:26786136
A MOTIF-BASED METHOD FOR PREDICTING INTERFACIAL RESIDUES IN BOTH THE RNA AND PROTEIN COMPONENTS OF PROTEIN-RNA COMPLEXES. PMID:26776208
Time dependence of evolutionary metrics during the 2009 pandemic influenza virus outbreak. PMID:26770819
Molecular docking analysis of known flavonoids as duel COX-2 inhibitors in the context of cancer. PMID:26770028
Type VI secretion systems of human gut Bacteroidales segregate into three genetic architectures, two of which are contained on mobile genetic elements. PMID:26768901
Revealing the Effects of Missense Mutations Causing Snyder-Robinson Syndrome on the Stability and Dimerization of Spermine Synthase. PMID:26761001
The Quaternary Structure of a Glycoside Hydrolase Dictates Specificity toward β-Glucans. PMID:26755730
A dynamic Asp-Arg interaction is essential for catalysis in microsomal prostaglandin E2 synthase. PMID:26755582
A dynamic Asp-Arg interaction is essential for catalysis in microsomal prostaglandin E2 synthase. PMID:26755582
Molecular dynamics simulation and bioinformatics study on chloroplast stromal ridge complex from rice (Oryza sativa L.). PMID:26753869
MS3ALIGN: an efficient molecular surface aligner using the topology of surface curvature. PMID:26753741
FIH Regulates Cellular Metabolism through Hydroxylation of the Deubiquitinase OTUB1. PMID:26752685
Rsite2: an efficient computational method to predict the functional sites of noncoding RNAs. PMID:26751501
New Dynamic Rotamer Libraries: Data-Driven Analysis of Side-Chain Conformational Propensities. PMID:26745530
Homology-Based Prediction of Potential Protein-Protein Interactions between Human Erythrocytes and Plasmodium falciparum. PMID:26740742
Why do Sequence Signatures Predict Enzyme Mechanism? Homology versus Chemistry. PMID:26740739
Integrating population variation and protein structural analysis to improve clinical interpretation of missense variation: application to the WD40 domain. PMID:26740553
Conformational Sampling and Binding Site Assessment of Suppression of Tumorigenicity 2 Ectodomain. PMID:26735493
Conformational space of clindamycin studied by ab initio and full-atom molecular dynamics. PMID:26733483
The TIM Barrel Architecture Facilitated the Early Evolution of Protein-Mediated Metabolism. PMID:26733481
Tripartite degrons confer diversity and specificity on regulated protein degradation in the ubiquitin-proteasome system. PMID:26732515
Progress in protein crystallography. PMID:26732246
dEMBF: A Comprehensive Database of Enzymes of Microalgal Biofuel Feedstock. PMID:26727469
The solution structural ensembles of RNA kink-turn motifs and their protein complexes. PMID:26727239
Fortilin potentiates the peroxidase activity of Peroxiredoxin-1 and protects against alcohol-induced liver damage in mice. PMID:26726832
Distributions of experimental protein structures on coarse-grained free energy landscapes. PMID:26723638
Are protein-protein interfaces special regions on a protein's surface? PMID:26723634
Constraint methods that accelerate free-energy simulations of biomolecules. PMID:26723628
Predictive energy landscapes for folding membrane protein assemblies. PMID:26723586
Short peptides from leucyl-tRNA synthetase rescue disease-causing mitochondrial tRNA point mutations. PMID:26721932
Understanding TRPV1 activation by ligands: Insights from the binding modes of capsaicin and resiniferatoxin. PMID:26719417
How Intrinsic Molecular Dynamics Control Intramolecular Communication in Signal Transducers and Activators of Transcription Factor STAT5. PMID:26717567
Entrapment of a Histone Tail by a DNA Lesion in a Nucleosome Suggests the Lesion Impacts Epigenetic Marking: A Molecular Dynamics Study. PMID:26709619
Computer-Aided Design of Orally Bioavailable Pyrrolidine Carboxamide Inhibitors of Enoyl-Acyl Carrier Protein Reductase of Mycobacterium tuberculosis with Favorable Pharmacokinetic Profiles. PMID:26703572
Pharmacophore Models and Pharmacophore-Based Virtual Screening: Concepts and Applications Exemplified on Hydroxysteroid Dehydrogenases. PMID:26703541
Dynamic Coupling and Allosteric Networks in the α Subunit of Heterotrimeric G Proteins. PMID:26703464
High-throughput screening against ~6.1 million structurally diverse, lead-like compounds to discover novel ROCK inhibitors for cerebral injury recovery. PMID:26700101
Network-Based Isoform Quantification with RNA-Seq Data for Cancer Transcriptome Analysis. PMID:26699225
Prediction of Protein-Protein Interaction Sites Based on Naive Bayes Classifier. PMID:26697220
Forward Individualized Medicine from Personal Genomes to Interactomes. PMID:26696898
Classification epitopes in groups based on their protein family. PMID:26696329
Thermostabilization of the Human Serotonin Transporter in an Antidepressant-Bound Conformation. PMID:26695939
Structural studies on molecular mechanisms of Nelfinavir resistance caused by non-active site mutation V77I in HIV-1 protease. PMID:26695135
PredβTM: A Novel β-Transmembrane Region Prediction Algorithm. PMID:26694538
Proteins and Their Interacting Partners: An Introduction to Protein-Ligand Binding Site Prediction Methods. PMID:26694353
The ETS Factor, ETV2: a Master Regulator for Vascular Endothelial Cell Development. PMID:26694034
Flexible CDOCKER: Development and application of a pseudo-explicit structure-based docking method within CHARMM. PMID:26691274
Local Geometry and Evolutionary Conservation of Protein Surfaces Reveal the Multiple Recognition Patches in Protein-Protein Interactions. PMID:26690684
Ribosome Mechanics Informs about Mechanism. PMID:26687034
Integration of structural dynamics and molecular evolution via protein interaction networks: a new era in genomic medicine. PMID:26684487
An Amphiphysin-Like Domain in Fus2p Is Required for Rvs161p Interaction and Cortical Localization. PMID:26681517
A systematic analysis of a broadly neutralizing antibody AR3C epitopes on Hepatitis C virus E2 envelope glycoprotein and their cross-reactivity. PMID:26681161
Discrete structural features among interface residue-level classes. PMID:26679043
Evaluation of free modeling targets in CASP11 and ROLL. PMID:26677002
Unraveling the distinctive features of hemorrhagic and non-hemorrhagic snake venom metalloproteinases using molecular simulations. PMID:26676823
Identification of Novel Fusion Inhibitors of Influenza A Virus by Chemical Genetics. PMID:26676787
Herbacetin Is a Novel Allosteric Inhibitor of Ornithine Decarboxylase with Antitumor Activity. PMID:26676750
Balancing Protein Stability and Activity in Cancer: A New Approach for Identifying Driver Mutations Affecting CBL Ubiquitin Ligase Activation. PMID:26676746
Rational design of α-helical tandem repeat proteins with closed architectures. PMID:26675735
The structural diversity of artificial genetic polymers. PMID:26673703
Computational insights into the interaction mechanism of triazolyl substituted tetrahydrobenzofuran derivatives with H(+),K(+)-ATPase at different pH. PMID:26667240
Ribosomal protein and biogenesis factors affect multiple steps during movement of the Saccharomyces cerevisiae Ty1 retrotransposon. PMID:26664557
Crystallographic education in the 21st century. PMID:26664347
Codon usage pattern in human SPANX genes. PMID:26664029
Protein purification and crystallization artifacts: The tale usually not told. PMID:26660914
Reads meet rotamers: structural biology in the age of deep sequencing. PMID:26658741
Structural and functional interactions between six-transmembrane μ-opioid receptors and β2-adrenoreceptors modulate opioid signaling. PMID:26657998
Systematic Prioritization of Druggable Mutations in ∼5000 Genomes Across 16 Cancer Types Using a Structural Genomics-based Approach. PMID:26657081
Understanding differences between synthetic and natural antibodies can help improve antibody engineering. PMID:26652053
Investigating the linkage between disease-causing amino acid variants and their effect on protein stability and binding. PMID:26650512
Text Mining for Protein Docking. PMID:26650466
Structural features determining thermal adaptation of esterases. PMID:26647400
Structural Insight into How Bacteria Prevent Interference between Multiple Divergent Type IV Secretion Systems. PMID:26646013
Topography of the TH5 Segment in the Diphtheria Toxin T-Domain Channel. PMID:26645703
Computational analysis reveal inhibitory action of nimbin against dengue viral envelope protein. PMID:26645034
The modulation of erythrocyte Na(+)/K(+)-ATPase activity by curcumin. PMID:26644941
Release of 50 new, drug-like compounds and their computational target predictions for open source anti-tubercular drug discovery. PMID:26642067
In Silico Investigation of Flavonoids as Potential Trypanosomal Nucleoside Hydrolase Inhibitors. PMID:26640486
Polarizable Atomic Multipole Solutes in a Generalized Kirkwood Continuum. PMID:26636202
On the role of steric clashes in methylation control of restriction endonuclease activity. PMID:26635397
Improving Protein Fold Recognition by Deep Learning Networks. PMID:26634993
AutoDockFR: Advances in Protein-Ligand Docking with Explicitly Specified Binding Site Flexibility. PMID:26629955
Specific Interaction between eEF1A and HIV RT Is Critical for HIV-1 Reverse Transcription and a Potential Anti-HIV Target. PMID:26624286
Dancing through Life: Molecular Dynamics Simulations and Network-Centric Modeling of Allosteric Mechanisms in Hsp70 and Hsp110 Chaperone Proteins. PMID:26619280
Crystal structure of CobK reveals strand-swapping between Rossmann-fold domains and molecular basis of the reduced precorrin product trap. PMID:26616290
Drug target prioritization by perturbed gene expression and network information. PMID:26615774
PDBFlex: exploring flexibility in protein structures. PMID:26615193
Towards improved genome-scale metabolic network reconstructions: unification, transcript specificity and beyond. PMID:26615025
Identification of potential inhibitors based on compound proposal contest: Tyrosine-protein kinase Yes as a target. PMID:26607293
From Single Variants to Protein Cascades: MULTISCALE MODELING OF SINGLE NUCLEOTIDE VARIANT SETS IN GENETIC DISORDERS. PMID:26601959
Characterization of Burkholderia pseudomallei protein BPSL1375 validates the Putative hemolytic activity of the COG3176 N-Acyltransferase family. PMID:26597807
Quantitative H2S-mediated protein sulfhydration reveals metabolic reprogramming during the integrated stress response. PMID:26595448
CHARMM-GUI HMMM Builder for Membrane Simulations with the Highly Mobile Membrane-Mimetic Model. PMID:26588561
Glabridin arrests cell cycle and inhibits proliferation of hepatocellular carcinoma by suppressing braf/MEK signaling pathway. PMID:26586395
An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system. PMID:26586237
Lightness Constancy in Surface Visualization. PMID:26584495
Experimental detection of short regulatory motifs in eukaryotic proteins: tips for good practice as well as for bad. PMID:26581338
Mutations in the KDM5C ARID Domain and Their Plausible Association with Syndromic Claes-Jensen-Type Disease. PMID:26580603
Coevolution Analysis of HIV-1 Envelope Glycoprotein Complex. PMID:26579711
Unexpected features of the dark proteome. PMID:26578815
Fold and flexibility: what can proteins' mechanical properties tell us about their folding nucleus? PMID:26577596
An amino acid code to define a protein's tertiary packing surface. PMID:26575337
Quantum effects in cation interactions with first and second coordination shell ligands in metalloproteins. PMID:26574284
Examining the assumptions underlying continuum-solvent models. PMID:26574250
Automated protein motif generation in the structure-based protein function prediction tool ProMOL. PMID:26573864
Macromolecular Modelling and Docking Simulations for the Discovery of Selective GPER Ligands. PMID:26573009
Using de novo protein structure predictions to measure the quality of very large multiple sequence alignments. PMID:26568625
Protein-protein interaction site prediction in Homo sapiens and E. coli using an interaction-affinity based membership function in fuzzy SVM. PMID:26564981
Computational drug design strategies applied to the modelling of human immunodeficiency virus-1 reverse transcriptase inhibitors. PMID:26560977
Attracting cavities for docking. Replacing the rough energy landscape of the protein by a smooth attracting landscape. PMID:26558715
Discovery and Characterization of a Potent Interleukin-6 Binding Peptide with Neutralizing Activity In Vivo. PMID:26555695
Differential Regulation of 6- and 7-Transmembrane Helix Variants of μ-Opioid Receptor in Response to Morphine Stimulation. PMID:26554831
Layers: A molecular surface peeling algorithm and its applications to analyze protein structures. PMID:26553411
Deciphering Supramolecular Structures with Protein-Protein Interaction Network Modeling. PMID:26549015
Gene Mutation Analysis in 253 Chinese Children with Unexplained Epilepsy and Intellectual/Developmental Disabilities. PMID:26544041
Computational Prediction of RNA-Binding Proteins and Binding Sites. PMID:26540053
Lessons from Hot Spot Analysis for Fragment-Based Drug Discovery. PMID:26538314
FireProt: Energy- and Evolution-Based Computational Design of Thermostable Multiple-Point Mutants. PMID:26529612
Problems of robustness in Poisson-Boltzmann binding free energies. PMID:26528091
Expanding the Catalytic Triad in Epoxide Hydrolases and Related Enzymes. PMID:26527505
On the accuracy of unit-cell parameters in protein crystallography. PMID:26527139
The twisted tauopathies: surface interactions of helically patterned filaments seen in alzheimer's disease and elsewhere. PMID:26526630
A Computational Model for Predicting Experimental RNA Nearest-Neighbor Free Energy Rankings: Inosine•Uridine Pairs. PMID:26525429
Narcolepsy-Associated HLA Class I Alleles Implicate Cell-Mediated Cytotoxicity. PMID:26518595
Composition of Overlapping Protein-Protein and Protein-Ligand Interfaces. PMID:26517868
Computational Identification of MoRFs in Protein Sequences Using Hierarchical Application of Bayes Rule. PMID:26517836
DisPredict: A Predictor of Disordered Protein Using Optimized RBF Kernel. PMID:26517719
244-MPT overcomes gefitinib resistance in non-small cell lung cancer cells. PMID:26517520
Identification of novel anti-hepatitis C virus agents by a quantitative high throughput screen in a cell-based infection assay. PMID:26515788
Molecular basis for the antagonistic activity of an anti-CXCR4 antibody. PMID:26514996
Clustering and percolation in protein loop structures. PMID:26510704
Understanding the fabric of protein crystals: computational classification of biological interfaces and crystal contacts. PMID:26508758
Association analyses of large-scale glycan microarray data reveal novel host-specific substructures in influenza A virus binding glycans. PMID:26508590
DynaFace: Discrimination between Obligatory and Non-obligatory Protein-Protein Interactions Based on the Complex's Dynamics. PMID:26506003
FluKB: A Knowledge-Based System for Influenza Vaccine Target Discovery and Analysis of the Immunological Properties of Influenza Viruses. PMID:26504853
PDID: database of molecular-level putative protein-drug interactions in the structural human proteome. PMID:26504143
Family resemblances: A common fold for some dimeric ion-coupled secondary transporters. PMID:26503722
Single-chain antibody-fragment M6P-1 possesses a mannose 6-phosphate monosaccharide-specific binding pocket that distinguishes N-glycan phosphorylation in a branch-specific manner†. PMID:26503547
CAB-Align: A Flexible Protein Structure Alignment Method Based on the Residue-Residue Contact Area. PMID:26502070
Targeting Mitogen-Activated Protein Kinase-Activated Protein Kinase 2 (MAPKAPK2, MK2): Medicinal Chemistry Efforts To Lead Small Molecule Inhibitors to Clinical Trials. PMID:26502061
Amino Acids in Nine Ligand-Prefer Ramachandran Regions. PMID:26491686
Computational Analysis of Amiloride Analogue Inhibitors of Coxsackievirus B3 RNA Polymerase. PMID:26491236
Methods for biological data integration: perspectives and challenges. PMID:26490630
Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways. PMID:26488417
Structural and Functional Characterization of the Enantiomers of the Antischistosomal Drug Oxamniquine. PMID:26485649
DNA binding protein identification by combining pseudo amino acid composition and profile-based protein representation. PMID:26482832
Dynamics-Driven Allostery in Protein Kinases. PMID:26481499
BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology. PMID:26481362
Energy Minimization on Manifolds for Docking Flexible Molecules. PMID:26478722
Predicting Large RNA-Like Topologies by a Knowledge-Based Clustering Approach. PMID:26478223
An Integrated Spin-Labeling/Computational-Modeling Approach for Mapping Global Structures of Nucleic Acids. PMID:26477260
Ensembles of a small number of conformations with relative populations. PMID:26474790
The Structural Basis for Activation and Inhibition of ZAP-70 Kinase Domain. PMID:26473606
BCL::Conf: small molecule conformational sampling using a knowledge based rotamer library. PMID:26473018
The utility of protein structure as a predictor of site-wise dN/dS varies widely among HIV-1 proteins. PMID:26468068
Computational prediction of protein interfaces: A review of data driven methods. PMID:26460190
Active-Site Plasticity Is Essential to Carbapenem Hydrolysis by OXA-58 Class D β-Lactamase of Acinetobacter baumannii. PMID:26459904
Recent contributions of structure-based drug design to the development of antibacterial compounds. PMID:26458180
Aqueous Molecular Dynamics Simulations of the M. tuberculosis Enoyl-ACP Reductase-NADH System and Its Complex with a Substrate Mimic or Diphenyl Ethers Inhibitors. PMID:26457706
Structural Insight into Fungal Cell Wall Recognition by a CVNH Protein with a Single LysM Domain. PMID:26455798
Unbiased View of Synaptic and Neuronal Gene Complement in Ctenophores: Are There Pan-neuronal and Pan-synaptic Genes across Metazoa? PMID:26454853
Nuclear Magnetic Resonance-Assisted Prediction of Secondary Structure for RNA: Incorporation of Direction-Dependent Chemical Shift Constraints. PMID:26451676
Ligand similarity guided receptor selection enhances docking accuracy and recall for non-nucleoside HIV reverse transcriptase inhibitors. PMID:26450349
Sequence specificity between interacting and non-interacting homologs identifies interface residues--a homodimer and monomer use case. PMID:26449222
Structural principles for computational and de novo design of 4Fe-4S metalloproteins. PMID:26449207
Rational Design of Benzylidenehydrazinyl-Substituted Thiazole Derivatives as Potent Inhibitors of Human Dihydroorotate Dehydrogenase with in Vivo Anti-arthritic Activity. PMID:26443076
Enzyme-linked DNA dendrimer nanosensors for acetylcholine. PMID:26442999
Physicochemical characteristics of structurally determined metabolite-protein and drug-protein binding events with respect to binding specificity. PMID:26442281
Functional Advantages of Conserved Intrinsic Disorder in RNA-Binding Proteins. PMID:26439842
Engineering Proteins for Thermostability with iRDP Web Server. PMID:26436543
Binding interaction of a novel fluorophore with serum albumins: steady state fluorescence perturbation and molecular modeling analysis. PMID:26435894
Phytochemical composition, antiparasitic and α-glucosidase inhibition activities from Pelliciera rhizophorae. PMID:26435737
Sunflower (Helianthus annuus) fatty acid synthase complex: β-hydroxyacyl-[acyl carrier protein] dehydratase genes. PMID:26433735
Exploration of Novel Inhibitors for Class I Histone Deacetylase Isoforms by QSAR Modeling and Molecular Dynamics Simulation Assays. PMID:26431201
PyMine: a PyMOL plugin to integrate and visualize data for drug discovery. PMID:26429562
PatchSurfers: Two methods for local molecular property-based binding ligand prediction. PMID:26427548
A novel and widespread class of ketosynthase is responsible for the head-to-head condensation of two acyl moieties in bacterial pyrone biosynthesis. PMID:26425196
Direct-Coupling Analysis of nucleotide coevolution facilitates RNA secondary and tertiary structure prediction. PMID:26420827
Sequence and structure-based comparative analysis to assess, identify and improve the thermostability of penicillin G acylases. PMID:26419382
CSAR Benchmark Exercise 2013: Evaluation of Results from a Combined Computational Protein Design, Docking, and Scoring/Ranking Challenge. PMID:26419257
Novel 3-Substituted 7-Phenylpyrrolo[3,2-f]quinolin-9(6H)-ones as Single Entities with Multitarget Antiproliferative Activity. PMID:26418966
Intrinsically disordered caldesmon binds calmodulin via the "buttons on a string" mechanism. PMID:26417545
Novel inhibitor discovery against aromatase through virtual screening and molecular dynamic simulation: a computational approach in drug design. PMID:26417225
Combined 3D-QSAR modeling and molecular docking study on multi-acting quinazoline derivatives as HER2 kinase inhibitors. PMID:26417222
Mitochondrial ADP/ATP exchange inhibition: a novel off-target mechanism underlying ibipinabant-induced myotoxicity. PMID:26416158
PROKARYO: an illustrative and interactive computational model of the lactose operon in the bacterium Escherichia coli. PMID:26415599
AlloRep: A Repository of Sequence, Structural and Mutagenesis Data for the LacI/GalR Transcription Regulators. PMID:26410588
Substrate-Induced Allosteric Change in the Quaternary Structure of the Spermidine N-Acetyltransferase SpeG. PMID:26410587
pKa predictions for proteins, RNAs, and DNAs with the Gaussian dielectric function using DelPhi pKa. PMID:26408449
Ultrafast protein structure-based virtual screening with Panther. PMID:26407559
Preferred conformations of N-glycan core pentasaccharide in solution and in glycoproteins. PMID:26405106
Joint modeling of RNase footprint sequencing profiles for genome-wide inference of RNA structure. PMID:26400167
Adapalene inhibits the activity of cyclin-dependent kinase 2 in colorectal carcinoma. PMID:26398439
Comparison of the Internal Dynamics of Metalloproteases Provides New Insights on Their Function and Evolution. PMID:26397984
Coupling Protein Side-Chain and Backbone Flexibility Improves the Re-design of Protein-Ligand Specificity. PMID:26397464
bPE toolkit: toolkit for computational protein engineering. PMID:26396658
Statistical approach for lysosomal membrane proteins (LMPs) identification. PMID:26396655
Exploring peptide/MHC detachment processes using hierarchical natural move Monte Carlo. PMID:26395770
Structure-based energetics of protein interfaces guides foot-and-mouth disease virus vaccine design. PMID:26389739
Repeat-swap homology modeling of secondary active transporters: updated protocol and prediction of elevator-type mechanisms. PMID:26388773
Contribution of the distal pocket residue to the acyl-chain-length specificity of (R)-specific enoyl-coenzyme A hydratases from Pseudomonas spp. PMID:26386053
Docking simulations suggest that all-trans retinoic acid could bind to retinoid X receptors. PMID:26384496
High-Throughput Ligand Discovery Reveals a Sitewise Gradient of Diversity in Broadly Evolved Hydrophilic Fibronectin Domains. PMID:26383268
Serine 363 of a Hydrophobic Region of Archaeal Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase from Archaeoglobus fulgidus and Thermococcus kodakaraensis Affects CO2/O2 Substrate Specificity and Oxygen Sensitivity. PMID:26381513
Orchestration of ErbB3 signaling through heterointeractions and homointeractions. PMID:26378253
Novel application of luciferase assay for the in vitro functional assessment of KAL1 variants in three females with septo-optic dysplasia (SOD). PMID:26375424
Protein-Protein Interfaces in Viral Capsids Are Structurally Unique. PMID:26375252
Introducing DInaMo: A Package for Calculating Protein Circular Dichroism Using Classical Electromagnetic Theory. PMID:26370961
An amino acid code for irregular and mixed protein packing. PMID:26370334
The glucocorticoid mometasone furoate is a novel FXR ligand that decreases inflammatory but not metabolic gene expression. PMID:26369990
How to resolve microsecond current fluctuations in single ion channels: the power of beta distributions. PMID:26368656
Probing binding hot spots at protein-RNA recognition sites. PMID:26365245
Co-LncRNA: investigating the lncRNA combinatorial effects in GO annotations and KEGG pathways based on human RNA-Seq data. PMID:26363020
An isomorphous replacement method for efficient de novo phasing for serial femtosecond crystallography. PMID:26360462
Selective Negative Allosteric Modulation Of Metabotropic Glutamate Receptors – A Structural Perspective of Ligands and Mutants. PMID:26359761
Electrostatic Interactions between Complement Regulator CD46(SCR1-2) and Adenovirus Ad11/Ad21 Fiber Protein Knob. PMID:26357573
A Fluorescent, Reagentless Biosensor for ATP, Based on Malonyl-Coenzyme A Synthetase. PMID:26355992
Accelerating molecular simulations of proteins using Bayesian inference on weak information. PMID:26351667
Computational approaches to study the effects of small genomic variations. PMID:26350246
Protein structure prediction using residue- and fragment-environment potentials in CASP11. PMID:26344195
The Landscape of Intertwined Associations in Homooligomeric Proteins. PMID:26340815
Resistance to Nucleotide Excision Repair of Bulky Guanine Adducts Opposite Abasic Sites in DNA Duplexes and Relationships between Structure and Function. PMID:26340000
Toward Automated Benchmarking of Atomistic Force Fields: Neat Liquid Densities and Static Dielectric Constants from the ThermoML Data Archive. PMID:26339862
AcconPred: Predicting Solvent Accessibility and Contact Number Simultaneously by a Multitask Learning Framework under the Conditional Neural Fields Model. PMID:26339631
Allosteric Dynamic Control of Binding. PMID:26338442
Dimeric interactions and complex formation using direct coevolutionary couplings. PMID:26338201
General overview on structure prediction of twilight-zone proteins. PMID:26338054
SFESA: a web server for pairwise alignment refinement by secondary structure shifts. PMID:26335387
A Web Resource for Standardized Benchmark Datasets, Metrics, and Rosetta Protocols for Macromolecular Modeling and Design. PMID:26335248
p38α MAPK and Type I Inhibitors: Binding Site Analysis and Use of Target Ensembles in Virtual Screening. PMID:26334265
Molecular level understanding of resistance to nalidixic acid in Salmonella enteric serovar typhimurium associates with the S83F sequence type. PMID:26329667
Integrated visual analysis of protein structures, sequences, and feature data. PMID:26329268
An Integrated Framework Advancing Membrane Protein Modeling and Design. PMID:26325167
Computational evaluation of phytocompounds for combating drug resistant tuberculosis by multi-targeted therapy. PMID:26323856
Structural characterization and modeling of the Borrelia burgdorferi hybrid histidine kinase Hk1 periplasmic sensor: A system for sensing small molecules associated with tick feeding. PMID:26321039
Structural Basis for the Discriminative Recognition of N6-Methyladenosine RNA by the Human YT521-B Homology Domain Family of Proteins. PMID:26318451
Citing a Data Repository: A Case Study of the Protein Data Bank. PMID:26317409
The value of protein structure classification information-Surveying the scientific literature. PMID:26313554
Weak conservation of structural features in the interfaces of homologous transient protein-protein complexes. PMID:26311309
Accurate Ab Initio and Template-Based Prediction of Short Intrinsically-Disordered Regions by Bidirectional Recurrent Neural Networks Trained on Large-Scale Datasets. PMID:26307973
Considerations of Protein Subpockets in Fragment-Based Drug Design. PMID:26307335
Advances in computational approaches for prioritizing driver mutations and significantly mutated genes in cancer genomes. PMID:26307061
RAG-3D: a search tool for RNA 3D substructures. PMID:26304547
Discovery of an essential nucleotidylating activity associated with a newly delineated conserved domain in the RNA polymerase-containing protein of all nidoviruses. PMID:26304538
Cardiolipin Interactions with Proteins. PMID:26300339
Double Variational Binding--(SMILES) Conformational Analysis by Docking Mechanisms for Anti-HIV Pyrimidine Ligands. PMID:26295229
A community resource of experimental data for NMR / X-ray crystal structure pairs. PMID:26293815
CoMOGrad and PHOG: From Computer Vision to Fast and Accurate Protein Tertiary Structure Retrieval. PMID:26293226
New insights into PDE4B inhibitor selectivity: CoMFA analyses and molecular docking studies. PMID:26290462
TMalphaDB and TMbetaDB: web servers to study the structural role of sequence motifs in α-helix and β-barrel domains of membrane proteins. PMID:26289158
Virtual Screening and Biological Validation of Novel Influenza Virus PA Endonuclease Inhibitors. PMID:26288686
Dead-End Elimination with a Polarizable Force Field Repacks PCNA Structures. PMID:26287633
Adaptation of the Mitochondrial Genome in Cephalopods: Enhancing Proton Translocation Channels and the Subunit Interactions. PMID:26285039
Structure-based Design of Peptides with High Affinity and Specificity to HER2 Positive Tumors. PMID:26284145
Conjugates of γ-Carbolines and Phenothiazine as new selective inhibitors of butyrylcholinesterase and blockers of NMDA receptors for Alzheimer Disease. PMID:26281952
Progressive Hemorrhage and Myotoxicity Induced by Echis carinatus Venom in Murine Model: Neutralization by Inhibitor Cocktail of N,N,N',N'-Tetrakis (2-Pyridylmethyl) Ethane-1,2-Diamine and Silymarin. PMID:26274501
Protein dynamics and the all-ferrous [Fe4 S4 ] cluster in the nitrogenase iron protein. PMID:26271353
Recognition of Damaged DNA for Nucleotide Excision Repair: A Correlated Motion Mechanism with a Mismatched cis-syn Thymine Dimer Lesion. PMID:26270861
Chemodetection and Destruction of Host Urea Allows Helicobacter pylori to Locate the Epithelium. PMID:26269952
Changes to the dynamic nature of hemagglutinin and the emergence of the 2009 pandemic H1N1 influenza virus. PMID:26269288
MultiSETTER: web server for multiple RNA structure comparison. PMID:26264783
PINGU: PredIction of eNzyme catalytic residues usinG seqUence information. PMID:26261982
An excess of catalytically required motions inhibits the scavenger decapping enzyme. PMID:26258763
High-throughput cellular RNA device engineering. PMID:26258292
Reconstruction of the temporal signaling network in Salmonella-infected human cells. PMID:26257716
RNA-binding residues prediction using structural features. PMID:26254826
Modularity of Protein Folds as a Tool for Template-Free Modeling of Structures. PMID:26252221
High-resolution crystal structure of cAMP-dependent protein kinase from Cricetulus griseus. PMID:26249705
Structural basis for drug-induced allosteric changes to human β-cardiac myosin motor activity. PMID:26246073
Protonation of Glu(135) Facilitates the Outward-to-Inward Structural Transition of Fucose Transporter. PMID:26244736
Computational Analysis of SAXS Data Acquisition. PMID:26244255
Siderocalin-mediated recognition, sensitization, and cellular uptake of actinides. PMID:26240330
Sequence and Structure Analysis of Biological Molecules Based on Computational Methods. PMID:26236729
Functional and Structural Consequences of Damaging Single Nucleotide Polymorphisms in Human Prostate Cancer Predisposition Gene RNASEL. PMID:26236721
Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2. PMID:26231283
Interdomain Contacts Control Native State Switching of RfaH on a Dual-Funneled Landscape. PMID:26230837
New Frontiers in Druggability. PMID:26230724
Evaluation of Trichodysplasia Spinulosa-Associated Polyomavirus Capsid Protein as a New Carrier for Construction of Chimeric Virus-Like Particles Harboring Foreign Epitopes. PMID:26230706
High Resolution Prediction of Calcium-Binding Sites in 3D Protein Structures Using FEATURE. PMID:26226489
Enzyme Selectivity of HIV Reverse Transcriptase: Conformations, Ligands, and Free Energy Partition. PMID:26225641
Constructing sequence-dependent protein models using coevolutionary information. PMID:26223372
An Effective Approach for Clustering InhA Molecular Dynamics Trajectory Using Substrate-Binding Cavity Features. PMID:26218832
Globular and disordered-the non-identical twins in protein-protein interactions. PMID:26217672
Structures and Functions of the Multiple KOW Domains of Transcription Elongation Factor Spt5. PMID:26217010
Fractal Dimensions of Macromolecular Structures. PMID:26213587
How can Databases assist with the Prediction of Chemical Compounds? PMID:26213422
Geometric analysis characterizes molecular rigidity in generic and non-generic protein configurations. PMID:26213417
A Newcomer's Guide to Peptide Crystallography. PMID:26213415
Structural Perspectives on the Evolutionary Expansion of Unique Protein-Protein Binding Sites. PMID:26213149
Molecular docking and structure-based drug design strategies. PMID:26205061
Intermolecular Complementation between Two Varicella-Zoster Virus pORF30 Terminase Domains Essential for DNA Encapsidation. PMID:26202238
An Overview of Practical Applications of Protein Disorder Prediction and Drive for Faster, More Accurate Predictions. PMID:26198229
Hole hopping through tyrosine/tryptophan chains protects proteins from oxidative damage. PMID:26195784
Quantifying evolutionary constraints on B-cell affinity maturation. PMID:26194758
Genome-wide characterization and expression analysis of common bean bHLH transcription factors in response to excess salt concentration. PMID:26193947
BALL-SNP: combining genetic and structural information to identify candidate non-synonymous single nucleotide polymorphisms. PMID:26191084
How an Inhibitor Bound to Subunit Interface Alters Triosephosphate Isomerase Dynamics. PMID:26190635
Quantitative Analysis of the Association Angle between T-cell Receptor Vα/Vβ Domains Reveals Important Features for Epitope Recognition. PMID:26185983
STAR3D: a stack-based RNA 3D structural alignment tool. PMID:26184875
DSSR: an integrated software tool for dissecting the spatial structure of RNA. PMID:26184874
Structural and Dynamical Insight into PPARγ Antagonism: In Silico Study of the Ligand-Receptor Interactions of Non-Covalent Antagonists. PMID:26184155
Virtual Screening and Molecular Dynamics Study of Potential Negative Allosteric Modulators of mGluR1 from Chinese Herbs. PMID:26184151
Structure alignment of membrane proteins: Accuracy of available tools and a consensus strategy. PMID:26178143
Adaptive evolution and elucidating the potential inhibitor against schizophrenia to target DAOA (G72) isoforms. PMID:26170631
Conformational thermostabilisation of corticotropin releasing factor receptor 1. PMID:26159865
Multi-level machine learning prediction of protein-protein interactions in Saccharomyces cerevisiae. PMID:26157620
A Multi-Objective Approach for Protein Structure Prediction Based on an Energy Model and Backbone Angle Preferences. PMID:26151847
New method to compute Rcomplete enables maximum likelihood refinement for small datasets. PMID:26150515
In Silico Identification and In Vitro and In Vivo Validation of Anti-Psychotic Drug Fluspirilene as a Potential CDK2 Inhibitor and a Candidate Anti-Cancer Drug. PMID:26147897
Structural Rigidity and Protein Thermostability in Variants of Lipase A from Bacillus subtilis. PMID:26147762
Predicting Binding Free Energy Change Caused by Point Mutations with Knowledge-Modified MM/PBSA Method. PMID:26146996
Molecular Characterization of LubX: Functional Divergence of the U-Box Fold by Legionella pneumophila. PMID:26146184
100 Years later: Celebrating the contributions of x-ray crystallography to allergy and clinical immunology. PMID:26145985
Protonation and geometry of histidine rings. PMID:26143916
Analysis and Ranking of Protein-Protein Docking Models Using Inter-Residue Contacts and Inter-Molecular Contact Maps. PMID:26140438
A Spectroscopy Approach for the Study of the Interaction of Oxovanadium(IV)-Salen Complexes with Proteins. PMID:26139532
RNA Structures as Mediators of Neurological Diseases and as Drug Targets. PMID:26139368
Conformational Entropy of Intrinsically Disordered Proteins from Amino Acid Triads. PMID:26138206
Structural basis for catalytically restrictive dynamics of a high-energy enzyme state. PMID:26138143
Hydrogen Exchange Mass Spectrometry of Proteins at Langmuir Monolayers. PMID:26134943
Capturing coevolutionary signals inrepeat proteins. PMID:26134293
Linking structural features of protein complexes and biological function. PMID:26131659
SInCRe-structural interactome computational resource for Mycobacterium tuberculosis. PMID:26130660
Comparison of intrinsic dynamics of cytochrome p450 proteins using normal mode analysis. PMID:26130403
De novo mutations in KIF1A cause progressive encephalopathy and brain atrophy. PMID:26125038
3,3'-Diindolylmethane (DIM) and its ring-substituted halogenated analogs (ring-DIMs) induce differential mechanisms of survival and death in androgen-dependent and -independent prostate cancer cells. PMID:26124925
Molecular docking and simulation of Curcumin with Geranylgeranyl Transferase1 (GGTase1) and Farnesyl Transferase (FTase). PMID:26124569
NMR structure calculation for all small molecule ligands and non-standard residues from the PDB Chemical Component Dictionary. PMID:26123317
Application of whole genome and RNA sequencing to investigate the genomic landscape of common variable immunodeficiency disorders. PMID:26122175
Non-canonical Bromodomain within DNA-PKcs Promotes DNA Damage Response and Radioresistance through Recognizing an IR-Induced Acetyl-Lysine on H2AX. PMID:26119999
Structure-Based Design of Inhibitors of Protein-Protein Interactions: Mimicking Peptide Binding Epitopes. PMID:26119925
Carbohydrates in Cyberspace. PMID:26113848
Physical Features of Intracellular Proteins that Moonlight on the Cell Surface. PMID:26110848
Substrate channeling between the human dihydrofolate reductase and thymidylate synthase. PMID:26096018
Building a virtual ligand screening pipeline using free software: a survey. PMID:26094053
Cooperative Electrostatic Interactions Drive Functional Evolution in the Alkaline Phosphatase Superfamily. PMID:26091851
PPM_One: a static protein structure based chemical shift predictor. PMID:26091586
Overcoming Chemical, Biological, and Computational Challenges in the Development of Inhibitors Targeting Protein-Protein Interactions. PMID:26091166
Differences in the Access of Lesions to the Nucleotide Excision Repair Machinery in Nucleosomes. PMID:26091016
A step towards long-wavelength protein crystallography: subjecting protein crystals to a vacuum. PMID:26089765
Targeting Importin-α7 as a Therapeutic Approach against Pandemic Influenza Viruses. PMID:26085167
Computational and Biochemical Discovery of RSK2 as a Novel Target for Epigallocatechin Gallate (EGCG). PMID:26083344
Calculating an optimal box size for ligand docking and virtual screening against experimental and predicted binding pockets. PMID:26082804
Inhibition of Peroxidase Activity of Cytochrome c: De Novo Compound Discovery and Validation. PMID:26078313
iCataly-PseAAC: Identification of Enzymes Catalytic Sites Using Sequence Evolution Information with Grey Model GM (2,1). PMID:26077845
Molecular Determinants Underlying Binding Specificities of the ABL Kinase Inhibitors: Combining Alanine Scanning of Binding Hot Spots with Network Analysis of Residue Interactions and Coevolution. PMID:26075886
Protein flexibility in the light of structural alphabets. PMID:26075209
Antithrombotic Effects of Five Organic Extracts of Bangladeshi Plants In Vitro and Mechanisms in In Silico Models. PMID:26075001
MemProtMD: Automated Insertion of Membrane Protein Structures into Explicit Lipid Membranes. PMID:26073602
Comprehensive analysis of sequences of a protein switch. PMID:26073558
Using kernelized partial canonical correlation analysis to study directly coupled side chains and allostery in small G proteins. PMID:26072474
Large-scale model quality assessment for improving protein tertiary structure prediction. PMID:26072473
RNAssess--a web server for quality assessment of RNA 3D structures. PMID:26068469
Fragment-based exploration of binding site flexibility in Mycobacterium tuberculosis BioA. PMID:26068403
Computing translational diffusion and sedimentation coefficients: an evaluation of experimental data and programs. PMID:26066679
Checking the STEP-Associated Trafficking and Internalization of Glutamate Receptors for Reduced Cognitive Deficits: A Machine Learning Approach-Based Cheminformatics Study and Its Application for Drug Repurposing. PMID:26066505
Discovery of new small molecules inhibiting 67 kDa laminin receptor interaction with laminin and cancer cell invasion. PMID:26062445
Novel Drug Targets for Food-Borne Pathogen Campylobacter jejuni: An Integrated Subtractive Genomics and Comparative Metabolic Pathway Study. PMID:26061459
Alternatively Spliced Homologous Exons Have Ancient Origins and Are Highly Expressed at the Protein Level. PMID:26061177
Practical macromolecular cryocrystallography. PMID:26057787
The chromatin fiber: multiscale problems and approaches. PMID:26057099
An Ebola virus-centered knowledge base. PMID:26055098
Structural investigation of ginsenoside Rf with PPARγ major transcriptional factor of adipogenesis and its impact on adipocyte. PMID:26045687
Structural Basis of Clade-specific Engagement of SAMHD1 (Sterile α Motif and Histidine/Aspartate-containing Protein 1) Restriction Factors by Lentiviral Viral Protein X (Vpx) Virulence Factors. PMID:26045556
Energetic Calculations to Decipher pH-Dependent Oligomerization and Domain Swapping of Proteins. PMID:26043007
Structural Basis for Enhancement of Carbapenemase Activity in the OXA-51 Family of Class D β-Lactamases. PMID:26042471
Revealing protein-lncRNA interaction. PMID:26041786
Comparative evaluation of several docking tools for docking small molecule ligands to DC-SIGN. PMID:26040678
DockBench: An Integrated Informatic Platform Bridging the Gap between the Robust Validation of Docking Protocols and Virtual Screening Simulations. PMID:26035098
Protomers of protein hetero-oligomers tend to resemble each other more than expected. PMID:26034682
Conformational transition paths harbor structures useful for aiding drug discovery and understanding enzymatic mechanisms in protein kinases. PMID:26032746
Structural and kinetic characterization of recombinant 2-hydroxymuconate semialdehyde dehydrogenase from Pseudomonas putida G7. PMID:26032336
Crystallization, structural diversity and anisotropy effects in 2D arrays of icosahedral viruses. PMID:26029772
Insights into Disease-Associated Mutations in the Human Proteome through Protein Structural Analysis. PMID:26027735
Navigating 3D electron microscopy maps with EM-SURFER. PMID:26025554
Every Site Counts: Submitting Transcription Factor-Binding Site Information through the CollecTF Portal. PMID:26013488
Molecular dynamics simulation of triclinic lysozyme in a crystal lattice. PMID:26013419
Structural Basis for the Inhibition of Helicobacter pylori α-Carbonic Anhydrase by Sulfonamides. PMID:26010545
Coulombic free energy and salt ion association per phosphate of all-atom models of DNA oligomer: dependence on oligomer size. PMID:26005495
Advancements in therapeutically targeting orphan GPCRs. PMID:26005419
The hydrophobic temperature dependence of amino acids directly calculated from protein structures. PMID:26000449
Predicting flavin and nicotinamide adenine dinucleotide-binding sites in proteins using the fragment transformation method. PMID:26000290
All-Atom Internal Coordinate Mechanics (ICM) Force Field for Hexopyranoses and Glycoproteins. PMID:25999804
CleavPredict: A Platform for Reasoning about Matrix Metalloproteinases Proteolytic Events. PMID:25996941
Evolution of the Translocation and Assembly Module (TAM). PMID:25994932
Contribution of EGFR and ErbB-3 Heterodimerization to the EGFR Mutation-Induced Gefitinib- and Erlotinib-Resistance in Non-Small-Cell Lung Carcinoma Treatments. PMID:25993617
Identification of small-molecule inhibitors against SecA by structure-based virtual ligand screening. PMID:25990955
Development and validation of a docking-based virtual screening platform for the identification of new lactate dehydrogenase inhibitors. PMID:25988609
Anti-CD28 Antibody-Initiated Cytokine Storm in Canines. PMID:25988188
How round is a protein? Exploring protein structures for globularity using conformal mapping. PMID:25988167
Roles of solvent accessibility and gene expression in modeling protein sequence evolution. PMID:25987828
Protein structure prediction guided by crosslinking restraints--A systematic evaluation of the impact of the crosslinking spacer length. PMID:25986934
Ab initio coordination chemistry for nickel chelation motifs. PMID:25985439
ProtDCal: A program to compute general-purpose-numerical descriptors for sequences and 3D-structures of proteins. PMID:25982853
Structure and Biophysical Characterization of the S-Adenosylmethionine-dependent O-Methyltransferase PaMTH1, a Putative Enzyme Accumulating during Senescence of Podospora anserina. PMID:25979334
A Kazal-Type Serine Protease Inhibitor from the Defense Gland Secretion of the Subterranean Termite Coptotermes formosanus Shiraki. PMID:25978745
Insights into the Interactions of Fasciola hepatica Cathepsin L3 with a Substrate and Potential Novel Inhibitors through In Silico Approaches. PMID:25978322
DBDiaSNP: An Open-Source Knowledgebase of Genetic Polymorphisms and Resistance Genes Related to Diarrheal Pathogens. PMID:25978092
BCSearch: fast structural fragment mining over large collections of protein structures. PMID:25977292
The eukaryotic translation initiation regulator CDC123 defines a divergent clade of ATP-grasp enzymes with a predicted role in novel protein modifications. PMID:25976611
CONFOLD: Residue-residue contact-guided ab initio protein folding. PMID:25974172
Multiscale Modeling of Drug-induced Effects of ReDuNing Injection on Human Disease: From Drug Molecules to Clinical Symptoms of Disease. PMID:25973739
Progress and challenges in predicting protein interfaces. PMID:25971595
ChSeq: A database of chameleon sequences. PMID:25970262
PockDrug-Server: a new web server for predicting pocket druggability on holo and apo proteins. PMID:25956651
Peptide Binding to a PDZ Domain by Electrostatic Steering via Nonnative Salt Bridges. PMID:25954893
Molecular investigations into the mechanics of a muscle anchoring complex. PMID:25954889
A method of searching for related literature on protein structure analysis by considering a user's intention. PMID:25952498
A method of searching for related literature on protein structure analysis by considering a user's intention. PMID:25952498
Evidence for Positive Selection within the PgiC1 Locus in the Grass Festuca ovina. PMID:25946223
Using support vector machines to improve elemental ion identification in macromolecular crystal structures. PMID:25945580
The RCSB PDB "Molecule of the Month": Inspiring a Molecular View of Biology. PMID:25942442
Knowledge-guided docking: accurate prospective prediction of bound configurations of novel ligands using Surflex-Dock. PMID:25940276
Investigate the binding of catechins to trypsin using docking and molecular dynamics simulation. PMID:25938485
Structural Basis for Different Substrate Profiles of Two Closely Related Class D β-Lactamases and Their Inhibition by Halogens. PMID:25938261
novPTMenzy: a database for enzymes involved in novel post-translational modifications. PMID:25931459
Buried chloride stereochemistry in the Protein Data Bank. PMID:25928393
Footprints of optimal protein assembly strategies in the operonic structure of prokaryotes. PMID:25927816
Biochemical and In-silico Studies on Pectin Methylesterase from G9 Variety of Musa acuminata for Delayed Ripening. PMID:25926894
Structural Insights into the Neutralization Properties of the Fully Human, Anti-interferon Monoclonal Antibody Sifalimumab. PMID:25925951
Customised fragments libraries for protein structure prediction based on structural class annotations. PMID:25925397
Principal component analysis-based unsupervised feature extraction applied to in silico drug discovery for posttraumatic stress disorder-mediated heart disease. PMID:25925353
Insights on Structural Characteristics and Ligand Binding Mechanisms of CDK2. PMID:25918937
Ligand deconstruction: Why some fragment binding positions are conserved and others are not. PMID:25918377
Saccharomyces cerevisiae-based mutational analysis of the bc1 complex Qo site residue 279 to study the trade-off between atovaquone resistance and function. PMID:25918152
Manual classification strategies in the ECOD database. PMID:25917548
Prospective performance evaluation of selected common virtual screening tools. Case study: Cyclooxygenase (COX) 1 and 2. PMID:25916906
Machine-learning scoring functions for identifying native poses of ligands docked to known and novel proteins. PMID:25916860
Computational Tools for Interpreting Ion Channel pH-Dependence. PMID:25915903
Equilibrium molecular thermodynamics from Kirkwood sampling. PMID:25915525
DOCK 6: Impact of new features and current docking performance. PMID:25914306
Structural features of a 3' splice site in influenza a. PMID:25909229
Stock-based detection of protein oligomeric states in jsPISA. PMID:25908787
Predicting drug metabolism: experiment and/or computation? PMID:25907346
The ABC of Phytohormone Translocation. PMID:25905596
DnaK as Antibiotic Target: Hot Spot Residues Analysis for Differential Inhibition of the Bacterial Protein in Comparison with the Human HSP70. PMID:25905464
Proteochemometric modeling of the antigen-antibody interaction: new fingerprints for antigen, antibody and epitope-paratope interaction. PMID:25901362
High-resolution crystal structures of protein helices reconciled with three-centered hydrogen bonds and multipole electrostatics. PMID:25894612
Genome-wide identification and characterization of Fox genes in the silkworm, Bombyx mori. PMID:25893708
Phenylpropanoids and flavonoids from Phlomis kurdica as inhibitors of human lactate dehydrogenase. PMID:25890391
The observation of evolutionary interaction pattern pairs in membrane proteins. PMID:25887048
PDIviz: analysis and visualization of protein-DNA binding interfaces. PMID:25886981
Mason: a JavaScript web site widget for visualizing and comparing annotated features in nucleotide or protein sequences. PMID:25884379
Molecular docking and inhibition studies on the interactions of Bacopa monnieri's potent phytochemicals against pathogenic Staphylococcus aureus. PMID:25884228
I-TASSER server: new development for protein structure and function predictions. PMID:25883148
RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures. PMID:25883046
Mutations that Separate the Functions of the Proofreading Subunit of the Escherichia coli Replicase. PMID:25878065
A wrench in the works of human acetylcholinesterase: soman induced conformational changes revealed by molecular dynamics simulations. PMID:25874456
Clustering molecular dynamics trajectories for optimizing docking experiments. PMID:25873944
Antiprotozoal Nitazoxanide Derivatives: Synthesis, Bioassays and QSAR Study Combined with Docking for Mechanistic Insight. PMID:25872791
Major centers of motion in the large ribosomal RNAs. PMID:25870411
Zinc Binding to MG53 Protein Facilitates Repair of Injury to Cell Membranes. PMID:25869134
Effects of mutations on the molecular dynamics of oxygen escape from the dimeric hemoglobin of Scapharca inaequivalvis. PMID:25866622
Combined covalent-electrostatic model of hydrogen bonding improves structure prediction with Rosetta. PMID:25866491
Reliable resonance assignments of selected residues of proteins with known structure based on empirical NMR chemical shift prediction. PMID:25863893
Design, Synthesis, and Biological Evaluation of Tetra-Substituted Thiophenes as Inhibitors of p38α MAPK. PMID:25861571
Computational prediction of protein-protein interactions. PMID:25859943
Epitope-based peptide vaccine design and target site depiction against Ebola viruses: an immunoinformatics study. PMID:25857850
The FTMap family of web servers for determining and characterizing ligand-binding hot spots of proteins. PMID:25855957
Carboxylated acyclonucleosides: synthesis and RNase A inhibition. PMID:25854756
Comparative analysis of cystatin superfamily in platyhelminths. PMID:25853513
The phenotypic expression of mitochondrial tRNA-mutations can be modulated by either mitochondrial leucyl-tRNA synthetase or the C-terminal domain thereof. PMID:25852750
GSHSite: exploiting an iteratively statistical method to identify s-glutathionylation sites with substrate specificity. PMID:25849935
ISOB: A Database of Indigenous Snake Species of Bangladesh with respective known venom composition. PMID:25848172
Three minimal sequences found in Ebola virus genomes and absent from human DNA. PMID:25840045
A survey of current trends in computational drug repositioning. PMID:25832646
Analysis of common bean (Phaseolus vulgaris L., genotype BAT93) calmodulin cDNA using computational tools. PMID:25829797
Nucleotide sequence of Phaseolus vulgaris L. alcohol dehydrogenase encoding cDNA and three-dimensional structure prediction of the deduced protein. PMID:25829796
BCL::MP-fold: Membrane protein structure prediction guided by EPR restraints. PMID:25820805
Hidden relationships between metalloproteins unveiled by structural comparison of their metal sites. PMID:25820752
Molecular dynamics study of naturally existing cavity couplings in proteins. PMID:25816327
An in silico insight into novel therapeutic interaction of LTNF peptide-LT10 and design of structure based peptidomimetics for putative anti-diabetic activity. PMID:25816209
A comprehensive alanine-scanning mutagenesis study reveals roles for salt bridges in the structure and activity of Pseudomonas aeruginosa elastase. PMID:25815820
New insights into Hoogsteen base pairs in DNA duplexes from a structure-based survey. PMID:25813047
Can the natural diversity of quorum-sensing advance synthetic biology? PMID:25806368
ALK and ROS1 as a joint target for the treatment of lung cancer: a review. PMID:25806218
Potential role of glutathione in evolution of thiol-based redox signaling sites in proteins. PMID:25805991
Selection pressure in CD8⁺ T-cell epitopes in the pol gene of HIV-1 infected individuals in Colombia. A bioinformatic approach. PMID:25803098
Development of a machine learning method to predict membrane protein-ligand binding residues using basic sequence information. PMID:25802517
Combined automated NOE assignment and structure calculation with CYANA. PMID:25801209
Magnesium-binding architectures in RNA crystal structures: validation, binding preferences, classification and motif detection. PMID:25800744
Patterns of structural and sequence variation within isotype lineages of the Neisseria meningitidis transferrin receptor system. PMID:25800619
Hotspots in an obligate homodimeric anticancer target. Structural and functional effects of interfacial mutations in human thymidylate synthase. PMID:25798950
Predicting protein interface residues using easily accessible on-line resources. PMID:25797794
Systemic lupus erythematosus-associated neutrophil cytosolic factor 2 mutation affects the structure of NADPH oxidase complex. PMID:25795782
QSLiMFinder: improved short linear motif prediction using specific query protein data. PMID:25792551
Crystal structure of Helicobacter pylori pseudaminic acid biosynthesis N-acetyltransferase PseH: implications for substrate specificity and catalysis. PMID:25781966
Large-scale evolutionary analyses on SecB subunits of bacterial sec system. PMID:25775430
Neuroferritinopathy: From ferritin structure modification to pathogenetic mechanism. PMID:25772441
LS-VISM: A software package for analysis of biomolecular solvation. PMID:25766844
Complete atomistic model of a bacterial cytoplasm for integrating physics, biochemistry, and systems biology. PMID:25765281
Speed of conformational change: comparing explicit and implicit solvent molecular dynamics simulations. PMID:25762327
Strong nonadditivity as a key structure-activity relationship feature: distinguishing structural changes from assay artifacts. PMID:25760829
Aggregation risk prediction for antibodies and its application to biotherapeutic development. PMID:25760769
Application of data mining tools for classification of protein structural class from residue based averaged NMR chemical shifts. PMID:25758094
Modeling the interaction between quinolinate and the receptor for advanced glycation end products (RAGE): relevance for early neuropathological processes. PMID:25757085
An overview of the prediction of protein DNA-binding sites. PMID:25756377
Spectrofluorometric and molecular docking studies on the binding of curcumenol and curcumenone to human serum albumin. PMID:25756376
Interaction of artesunate with β-cyclodextrin: Characterization, thermodynamic parameters, molecular modeling, effect of PEG on complexation and antimalarial activity. PMID:25755980
Subknots in ideal knots, random knots, and knotted proteins. PMID:25753957
Molecular dynamics simulations of glycoproteins using CHARMM. PMID:25753723
A Deep Learning Network Approach to ab initio Protein Secondary Structure Prediction. PMID:25750595
Molecular docking to identify associations between drugs and class I human leukocyte antigens for predicting idiosyncratic drug reactions. PMID:25747444
BgN-Score and BsN-Score: bagging and boosting based ensemble neural networks scoring functions for accurate binding affinity prediction of protein-ligand complexes. PMID:25734685
Most highly expressed protein-coding genes have a single dominant isoform. PMID:25732134
Effective alignment of RNA pseudoknot structures using partition function posterior log-odds scores. PMID:25727492
Structural basis for self-assembly of a cytolytic pore lined by protein and lipid. PMID:25716479
Structural studies on Laz, a promiscuous anticancer Neisserial protein. PMID:25714335
A triple mutant in the Ω-loop of TEM-1 β-lactamase changes the substrate profile via a large conformational change and an altered general base for catalysis. PMID:25713062
3dRNAscore: a distance and torsion angle dependent evaluation function of 3D RNA structures. PMID:25712091
Fenretinide Perturbs Focal Adhesion Kinase in Premalignant and Malignant Human Oral Keratinocytes. Fenretinide's Chemopreventive Mechanisms Include ECM Interactions. PMID:25712051
Rock, paper, scissors: harnessing complementarity in ortholog detection methods improves comparative genomic inference. PMID:25711833
Versatile communication strategies among tandem WW domain repeats. PMID:25710931
Experimental characterization of adsorbed protein orientation, conformation, and bioactivity. PMID:25708632
Deciphering complex patterns of class-I HLA-peptide cross-reactivity via hierarchical grouping. PMID:25708537
Protein-protein docking on hardware accelerators: comparison of GPU and MIC architectures. PMID:25707855
Atomic-accuracy models from 4.5-Å cryo-electron microscopy data with density-guided iterative local refinement. PMID:25707030
Conformational B-cell epitope prediction method based on antigen preprocessing and mimotopes analysis. PMID:25705652
Prediction of the potency of mammalian cyclooxygenase inhibitors with ensemble proteochemometric modeling. PMID:25705261
MoDock: A multi-objective strategy improves the accuracy for molecular docking. PMID:25705248
AIDA: ab initio domain assembly for automated multi-domain protein structure prediction and domain-domain interaction prediction. PMID:25701568
SIRT5 regulation of ammonia-induced autophagy and mitophagy. PMID:25700560
Comparative structural analysis of the caspase family with other clan CD cysteine peptidases. PMID:25697094
Opposing orientations of the anti-psychotic drug trifluoperazine selected by alternate conformations of M144 in calmodulin. PMID:25694384
Quantifying the entropy of binding for water molecules in protein cavities by computing correlations. PMID:25692597
Comparison of three ionic liquid-tolerant cellulases by molecular dynamics. PMID:25692593
High-resolution crystal structure of Z-DNA in complex with Cr(3+) cations. PMID:25687556
The UCSC Ebola Genome Portal. PMID:25685613
A comprehensive immunoinformatics and target site study revealed the corner-stone toward Chikungunya virus treatment. PMID:25682054
Valproic acid as a potential inhibitor of Plasmodium falciparum histone deacetylase 1 (PfHDAC1): an in silico approach. PMID:25679451
A binding mode hypothesis of tiagabine confirms liothyronine effect on γ-aminobutyric acid transporter 1 (GAT1). PMID:25679268
Pooled sequencing of 531 genes in inflammatory bowel disease identifies an associated rare variant in BTNL2 and implicates other immune related genes. PMID:25671699
Molecular modeling and molecular dynamics simulation study of the human Rab9 and RhoBTB3 C-terminus complex. PMID:25670879
Models of protein-ligand crystal structures: trust, but verify. PMID:25665575
Local and macroscopic electrostatic interactions in single α-helices. PMID:25664692
The activator of apoptosis Smac-DIABLO acts as a tetramer in solution. PMID:25650938
Molecular epidemiology of influenza A virus infection among hospitalized children in Vietnam during post-pandemic period. PMID:25648607
xiNET: cross-link network maps with residue resolution. PMID:25648531
Modeling functional changes to Escherichia coli thymidylate synthase upon single residue replacements: a structure-based approach. PMID:25648456
ω-Hydroxyemodin limits staphylococcus aureus quorum sensing-mediated pathogenesis and inflammation. PMID:25645827
PCalign: a method to quantify physicochemical similarity of protein-protein interfaces. PMID:25638036
Aquaria: simplifying discovery and insight from protein structures. PMID:25633501
Annotation of proteins of unknown function: initial enzyme results. PMID:25630330
Binding mode analysis of zerumbone to key signal proteins in the tumor necrosis factor pathway. PMID:25629232
Prediction of distal residue participation in enzyme catalysis. PMID:25627867
Spatial analysis and quantification of the thermodynamic driving forces in protein-ligand binding: binding site variability. PMID:25625202
A novel polyamine allosteric site of SpeG from Vibrio cholerae is revealed by its dodecameric structure. PMID:25623305
Pharmacophore modeling improves virtual screening for novel peroxisome proliferator-activated receptor-gamma ligands. PMID:25616366
Zinc-substituted pseudoazurin solved by S/Zn-SAD phasing. PMID:25615962
Increasing the structural coverage of tuberculosis drug targets. PMID:25613812
Macromolecular ab initio phasing enforcing secondary and tertiary structure. PMID:25610631
Plant membrane assays with cytokinin receptors underpin the unique role of free cytokinin bases as biologically active ligands. PMID:25609827
Biocontainment of genetically modified organisms by synthetic protein design. PMID:25607366
An approach to creating a more realistic working model from a protein data bank entry. PMID:25605595
Systematic characterization and prediction of post-translational modification cross-talk. PMID:25605461
RNAMotifScanX: a graph alignment approach for RNA structural motif identification. PMID:25595715
Single-molecule dataset (SMD): a generalized storage format for raw and processed single-molecule data. PMID:25591752
Mapping the membrane topography of the TH6-TH7 segment of the diphtheria toxin T-domain channel. PMID:25582482
CASP10-BCL::Fold efficiently samples topologies of large proteins. PMID:25581562
An In Silico Approach towards the Prediction of Druglikeness Properties of Inhibitors of Plasminogen Activator Inhibitor1. PMID:25580120
Representation of Ion-Protein Interactions Using the Drude Polarizable Force-Field. PMID:25578354
Role of indirect readout mechanism in TATA box binding protein-DNA interaction. PMID:25575717
A survey of computational intelligence techniques in protein function prediction. PMID:25574395
Using isoelectric point to determine the pH for initial protein crystallization trials. PMID:25573921
Protein sector analysis for the clustering of disease-associated mutations. PMID:25559331
Highly selective salicylketoxime-based estrogen receptor β agonists display antiproliferative activities in a glioma model. PMID:25559213
High-density mapping of the MHC identifies a shared role for HLA-DRB1*01:03 in inflammatory bowel diseases and heterozygous advantage in ulcerative colitis. PMID:25559196
A three dimensional visualisation approach to protein heavy-atom structure reconstruction. PMID:25551190
Characterization of ambrette seed oil and its mode of action in bacteria. PMID:25551188
Evolutionary genomics and adaptive evolution of the Hedgehog gene family (Shh, Ihh and Dhh) in vertebrates. PMID:25549322
Identifying tandem Ankyrin repeats in protein structures. PMID:25547411
Refinement by shifting secondary structure elements improves sequence alignments. PMID:25546158
Metazoan remaining genes for essential amino acid biosynthesis: sequence conservation and evolutionary analyses. PMID:25545100
Generic GPCR residue numbers - aligning topology maps while minding the gaps. PMID:25541108
The chemical component dictionary: complete descriptions of constituent molecules in experimentally determined 3D macromolecules in the Protein Data Bank. PMID:25540181
Phylodynamic analysis of clinical and environmental Vibrio cholerae isolates from Haiti reveals diversification driven by positive selection. PMID:25538191
Sequence search and analysis of gene products containing RNA recognition motifs in the human genome. PMID:25534245
Macromolecular X-ray structure determination using weak, single-wavelength anomalous data. PMID:25532136
INTEGRATING COMPUTATIONAL PROTEIN FUNCTION PREDICTION INTO DRUG DISCOVERY INITIATIVES. PMID:25530654
Positioning of cysteine residues within the N-terminal portion of the BST-2/tetherin ectodomain is important for functional dimerization of BST-2. PMID:25525265
A graph kernel method for DNA-binding site prediction. PMID:25521807
Bhageerath-H: a homology/ab initio hybrid server for predicting tertiary structures of monomeric soluble proteins. PMID:25521245
Characterization and identification of protein O-GlcNAcylation sites with substrate specificity. PMID:25521204
Combining spatial and chemical information for clustering pharmacophores. PMID:25521061
Role of bifidobacteria in the hydrolysis of chlorogenic acid. PMID:25515139
Mycobacterium tuberculosis cell division protein, FtsE, is an ATPase in dimeric form. PMID:25511207
First co-expression of a lipase and its specific foldase obtained by metagenomics. PMID:25510188
Computational analysis and mapping of novel open reading frames in influenza A viruses. PMID:25506939
Inhibition of VEGF: a novel mechanism to control angiogenesis by Withania somnifera's key metabolite Withaferin A. PMID:25505656
Gradient Models in Molecular Biophysics: Progress, Challenges, Opportunities. PMID:25505358
Survival analysis of infected mice reveals pathogenic variations in the genome of avian H1N1 viruses. PMID:25503687
A massively parallel pipeline to clone DNA variants and examine molecular phenotypes of human disease mutations. PMID:25502805
Protein structure annotation resources. PMID:25502191
Protein-protein docking with dynamic residue protonation states. PMID:25501663
Diversification and distinctive structural features of S-RNase alleles in the genus Solanum. PMID:25501309
Genome-scale identification and characterization of moonlighting proteins. PMID:25497125
Structural basis for complementary and alternative medicine: Phytochemical interaction with non-structural protein 2 protease-a reverse engineering strategy. PMID:25491534
Intrinsically disordered and pliable Starmaker-like protein from medaka (Oryzias latipes) controls the formation of calcium carbonate crystals. PMID:25490041
Discovery of potential drugs for human-infecting H7N9 virus containing R294K mutation. PMID:25489236
Molecular docking and analgesic studies of Erythrina variegata׳s derived phytochemicals with COX enzymes. PMID:25489172
Achievements and challenges in structural bioinformatics and computational biophysics. PMID:25488929
Specificity rendering 'hot-spots' for aurora kinase inhibitor design: the role of non-covalent interactions and conformational transitions. PMID:25485544
Wavelet Analysis of Protein Motion. PMID:25484480
Conformational analysis of the DFG-out kinase motif and biochemical profiling of structurally validated type II inhibitors. PMID:25478866
Discovering co-occurring patterns and their biological significance in protein families. PMID:25474736
ECOD: an evolutionary classification of protein domains. PMID:25474468
Adjusting protein graphs based on graph entropy. PMID:25474347
DBBP: database of binding pairs in protein-nucleic acid interactions. PMID:25474259
A novel PI3K inhibitor PIK-C98 displays potent preclinical activity against multiple myeloma. PMID:25474140
Identification of single-stranded and double-stranded DNA binding proteins based on protein structure. PMID:25474071
Mapping hydrophobicity on the protein molecular surface at atom-level resolution. PMID:25462574
Conformational dynamics of a crystalline protein from microsecond-scale molecular dynamics simulations and diffuse X-ray scattering. PMID:25453071
A general computational approach for repeat protein design. PMID:25451037
Crosstalk between signaling pathways provided by single and multiple protein phosphorylation sites. PMID:25451034
Fe-S proteins that regulate gene expression. PMID:25450978
Enhanced sampling techniques in molecular dynamics simulations of biological systems. PMID:25450171
Antiplasmodial activity of chloroquine analogs against chloroquine-resistant parasites, docking studies and mechanisms of drug action. PMID:25440372
Transferable coarse-grained potential for de novo protein folding and design. PMID:25436908
Intrinsic disorder drives N-terminal ubiquitination by Ube2w. PMID:25436519
Plant-PrAS: a database of physicochemical and structural properties and novel functional regions in plant proteomes. PMID:25435546
Gene expression microarray analysis of the sciatic nerve of mice with diabetic neuropathy. PMID:25435094
Insights into the role of the unusual disulfide bond in copper-zinc superoxide dismutase. PMID:25433341
MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins. PMID:25431331
The RCSB Protein Data Bank: views of structural biology for basic and applied research and education. PMID:25428375
Structure-based network analysis of activation mechanisms in the ErbB family of receptor tyrosine kinases: the regulatory spine residues are global mediators of structural stability and allosteric interactions. PMID:25427151
Novel virtual screening approach for the discovery of human tyrosinase inhibitors. PMID:25426625
Comparative Structural and Functional Analysis of Staphylococcus aureus Glucokinase with other Bacterial Glucokinases. PMID:25425757
DFGmodel: predicting protein kinase structures in inactive states for structure-based discovery of type-II inhibitors. PMID:25420233
Adsorption-induced changes in ribonuclease A structure and enzymatic activity on solid surfaces. PMID:25420087
Lipid-linked oligosaccharides in membranes sample conformations that facilitate binding to oligosaccharyltransferase. PMID:25418169
Proton transfer in the K-channel analog of B-type Cytochrome c oxidase from Thermus thermophilus. PMID:25418102
A proteome-scale map of the human interactome network. PMID:25416956
Quantum Mechanics Approaches to Drug Research in the Era of Structural Chemogenomics. PMID:25414519
Human ALDH1B1 polymorphisms may affect the metabolism of acetaldehyde and all-trans retinaldehyde--in vitro studies and computational modeling. PMID:25413692
Structural aspects of fungal allergens. PMID:25413498
Trimeric structure of (+)-pinoresinol-forming dirigent protein at 1.95 Å resolution with three isolated active sites. PMID:25411250
Molecular mechanisms and design principles for promiscuous inhibitors to avoid drug resistance: lessons learned from HIV-1 protease inhibition. PMID:25410041
Genome-wide investigation and expression profiling of AP2/ERF transcription factor superfamily in foxtail millet (Setaria italica L.). PMID:25409524
Early chordate origin of the vertebrate integrin αI domains. PMID:25409021
PCP-ML: protein characterization package for machine learning. PMID:25406415
Improvements to REDCRAFT: a software tool for simultaneous characterization of protein backbone structure and dynamics from residual dipolar couplings. PMID:25403759
Homology models of the HIV-1 attachment inhibitor BMS-626529 bound to gp120 suggest a unique mechanism of action. PMID:25401969
Interferon lambda: opportunities, risks, and uncertainties in the fight against HCV. PMID:25400636
POVME 2.0: An Enhanced Tool for Determining Pocket Shape and Volume Characteristics. PMID:25400521
Interaction of the anticancer gallium(III) complexes of 8-hydroxyquinoline and maltol with human serum proteins. PMID:25398250
Rfam 12.0: updates to the RNA families database. PMID:25392425
DISOPRED3: precise disordered region predictions with annotated protein-binding activity. PMID:25391399
A molecular fragment cheminformatics roadmap for mesoscopic simulation. PMID:25383098
PolyprOnline: polyproline helix II and secondary structure assignment database. PMID:25380779
Identification of antipsychotic drug fluspirilene as a potential p53-MDM2 inhibitor: a combined computational and experimental study. PMID:25377899
BactPepDB: a database of predicted peptides from a exhaustive survey of complete prokaryote genomes. PMID:25377257
Structural model of the hUbA1-UbcH10 quaternary complex: in silico and experimental analysis of the protein-protein interactions between E1, E2 and ubiquitin. PMID:25375166
Characteristics of protein residue-residue contacts and their application in contact prediction. PMID:25374390
The structure of rice weevil pectin methylesterase. PMID:25372813
Isoliquiritigenin induces apoptosis and inhibits xenograft tumor growth of human lung cancer cells by targeting both wild type and L858R/T790M mutant EGFR. PMID:25368326
Asymmetric binding to NS5A by daclatasvir (BMS-790052) and analogs suggests two novel modes of HCV inhibition. PMID:25365735
B-factor Analysis and Conformational Rearrangement of Aldose Reductase. PMID:25364319
Functional consequences of somatic mutations in cancer using protein pocket-based prioritization approach. PMID:25360158
Multiscale approach to the determination of the photoactive yellow protein signaling state ensemble. PMID:25356903
BioGPS descriptors for rational engineering of enzyme promiscuity and structure based bioinformatic analysis. PMID:25353170
Molecular docking of fisetin with AD associated AChE, ABAD and BACE1 proteins. PMID:25352723
Contribution of phenylalanine side chain intercalation to the TATA-box binding protein-DNA interaction: molecular dynamics and dispersion-corrected density functional theory studies. PMID:25352516
Improving protein fold recognition by random forest. PMID:25350499
Investigating Molecular Mechanisms of Activation and Mutation of the HER2 Receptor Tyrosine Kinase through Computational Modeling and Simulation. PMID:25346782
Rice cytochrome P450 MAX1 homologs catalyze distinct steps in strigolactone biosynthesis. PMID:25344813
Computational design of protein-based inhibitors of Plasmodium vivax subtilisin-like 1 protease. PMID:25343504
Visualizing Validation of Protein Surface Classifiers. PMID:25342867
Global distribution of Chelonid fibropapilloma-associated herpesvirus among clinically healthy sea turtles. PMID:25342462
Molecular modeling of a tandem two pore domain potassium channel reveals a putative binding site for general anesthetics. PMID:25340635
Operating mechanism and molecular dynamics of pheromone-binding protein ASP1 as influenced by pH. PMID:25337796
Design of gem-difluoro-bis-tetrahydrofuran as P2 ligand for HIV-1 protease inhibitors to improve brain penetration: synthesis, X-ray studies, and biological evaluation. PMID:25336073
An integrated model of transcription factor diffusion shows the importance of intersegmental transfer and quaternary protein structure for target site finding. PMID:25333780
Molecular docking studies of anti-cancerous candidates in Hippophae rhamnoides and Hippophae salicifolia. PMID:25332713
The use of experimental structures to model protein dynamics. PMID:25330965
Apaf-1 inhibitors protect from unwanted cell death in in vivo models of kidney ischemia and chemotherapy induced ototoxicity. PMID:25330150
Efficient Maintenance and Update of Nonbonded Lists in Macromolecular Simulations. PMID:25328494
Src is a novel potential off-target of RXR agonists, 9-cis-UAB30 and Targretin, in human breast cancer cells. PMID:25328014
A PDB-wide, evolution-based assessment of protein-protein interfaces. PMID:25326082
Molecular dissection of Mycobacterium tuberculosis integration host factor reveals novel insights into the mode of DNA binding and nucleoid compaction. PMID:25324543
Molecular dynamics simulations of the Nip7 proteins from the marine deep- and shallow-water Pyrococcus species. PMID:25315147
Bayesian model of protein primary sequence for secondary structure prediction. PMID:25314659
Post-translational modifications of transthyretin affect the triiodonine-binding potential. PMID:25311081
Structural elucidation of the DFG-Asp in and DFG-Asp out states of TAM kinases and insight into the selectivity of their inhibitors. PMID:25310149
An Inductive Logic Programming Approach to Validate Hexose Binding Biochemical Knowledge. PMID:25309972
SkateBase, an elasmobranch genome project and collection of molecular resources for chondrichthyan fishes. PMID:25309735
Executing SADI services in Galaxy. PMID:25309716
Investigation of Changes in Tetracycline Repressor Binding upon Mutations in the Tetracycline Operator. PMID:25308994
Protein helical structure determination using CD spectroscopy for solutions with strong background absorbance from 190 to 230nm. PMID:25308773
Comparative genomic analysis of genogroup 1 (Wa-like) rotaviruses circulating in the USA, 2006-2009. PMID:25301114
Linear motif-mediated interactions have contributed to the evolution of modularity in complex protein interaction networks. PMID:25299147
Use of a structural alphabet to find compatible folds for amino acid sequences. PMID:25297700
EXIA2: web server of accurate and rapid protein catalytic residue prediction. PMID:25295274
Genome-wide identification and tissue-specific expression analysis of UDP-glycosyltransferases genes confirm their abundance in Cicer arietinum (Chickpea) genome. PMID:25290312
BFMP: a method for discretizing and visualizing pyranose conformations. PMID:25289680
A drunken search in crystallization space. PMID:25286930
Archiving raw crystallographic data. PMID:25286835
Efficient cryoprotection of macromolecular crystals using vapor diffusion of volatile alcohols. PMID:25286441
Thiolation-enhanced substrate recognition by D-alanyl carrier protein ligase DltA from Bacillus cereus. PMID:25285205
Celastrol inhibits Plasmodium falciparum enoyl-acyl carrier protein reductase. PMID:25284249
Computational biophysical, biochemical, and evolutionary signature of human R-spondin family proteins, the member of canonical Wnt/β-catenin signaling pathway. PMID:25276837
Saccharin sulfonamides as inhibitors of carbonic anhydrases I, II, VII, XII, and XIII. PMID:25276805
Evidence of conformational selection driving the formation of ligand binding sites in protein-protein interfaces. PMID:25275445
CSI 2.0: a significantly improved version of the Chemical Shift Index. PMID:25273503
Polyphony: superposition independent methods for ensemble-based drug discovery. PMID:25265915
The P-loop region of Schlafen 3 acts within the cytosol to induce differentiation of human Caco-2 intestinal epithelial cells. PMID:25261706
The role of the interactome in the maintenance of deleterious variability in human populations. PMID:25261458
Modeling T cell receptor recognition of CD1-lipid and MR1-metabolite complexes. PMID:25260513
A tripartite cocktail of chimeric monoclonal antibodies passively protects mice against ricin, staphylococcal enterotoxin B and Clostridium perfringens epsilon toxin. PMID:25260254
Pharmacological relevance of endoxifen in a laboratory simulation of breast cancer in postmenopausal patients. PMID:25258390
Ontogeny of recognition specificity and functionality for the broadly neutralizing anti-HIV antibody 4E10. PMID:25254371
Amino acid sequence and structural comparison of BACE1 and BACE2 using evolutionary trace method. PMID:25254246
Drug-Like Protein-Protein Interaction Modulators: Challenges and Opportunities for Drug Discovery and Chemical Biology. PMID:25254076
Origins of fluorescence in evolved bacteriophytochromes. PMID:25253687
Structure-based inhibition of protein-protein interactions. PMID:25253637
Interactions Among Plant Transcription Factors Regulating Expression of Stress-responsive Genes. PMID:25249757
Multiple influenza A (H3N2) mutations conferring resistance to neuraminidase inhibitors in a bone marrow transplant recipient. PMID:25246391
Expanding the Halohydrin Dehalogenase Enzyme Family: Identification of Novel Enzymes by Database Mining. PMID:25239895
A multi-scale-multi-stable model for the rhodopsin photocycle. PMID:25237751
FixingTIM: interactive exploration of sequence and structural data to identify functional mutations in protein families. PMID:25237390
Nature versus design: the conformational propensities of D-amino acids and the importance of side chain chirality. PMID:25233851
Examining variable domain orientations in antigen receptors gives insight into TCR-like antibody design. PMID:25233457
eMatchSite: sequence order-independent structure alignments of ligand binding pockets in protein models. PMID:25232727
Computational survey of peptides derived from disulphide-bonded protein loops that may serve as mediators of protein-protein interactions. PMID:25231912
Pharmacophore-based similarity scoring for DOCK. PMID:25229837
Frustration in biomolecules. PMID:25225856
A new set of atomic radii for accurate estimation of solvation free energy by Poisson-Boltzmann solvent model. PMID:25220475
Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC). PMID:25219455
Global analysis of protein structural changes in complex proteomes. PMID:25218519
In silico discovery of potential VEGFR-2 inhibitors from natural derivatives for anti-angiogenesis therapy. PMID:25216334
The structural biology of phenazine biosynthesis. PMID:25215885
Combining structure-based pharmacophore modeling, virtual screening, and in silico ADMET analysis to discover novel tetrahydro-quinoline based pyruvate kinase isozyme M2 activators with antitumor activity. PMID:25214764
The structural basis of ATP as an allosteric modulator. PMID:25211773
Duplication of genes in an ATP-binding cassette transport system increases dynamic range while maintaining ligand specificity. PMID:25210043
Phage display creates innovative applications to combat hepatitis B virus. PMID:25206271
Accurate single-sequence prediction of solvent accessible surface area using local and global features. PMID:25204636
Sunflower (Helianthus annuus) fatty acid synthase complex: enoyl-[acyl carrier protein]-reductase genes. PMID:25204631
AUTO-MUTE 2.0: A Portable Framework with Enhanced Capabilities for Predicting Protein Functional Consequences upon Mutation. PMID:25197272
Molecular replacement with a large number of molecules in the asymmetric unit. PMID:25195913
High-resolution structure of a membrane protein transferred from amphipol to a lipidic mesophase. PMID:25192977
Adverse drug reaction prediction using scores produced by large-scale drug-protein target docking on high-performance computing machines. PMID:25191698
Effects of light and the regulatory B-subunit composition of protein phosphatase 2A on the susceptibility of Arabidopsis thaliana to aphid (Myzus persicae) infestation. PMID:25191331
Enhancing protein-vitamin binding residues prediction by multiple heterogeneous subspace SVMs ensemble. PMID:25189131
Design of an epitope-based peptide vaccine against spike protein of human coronavirus: an in silico approach. PMID:25187696
On methods for determining solvent accessible surface area for proteins in their unfolded state. PMID:25187400
An atomic model of brome mosaic virus using direct electron detection and real-space optimization. PMID:25185801
RCSB PDB Mobile: iOS and Android mobile apps to provide data access and visualization to the RCSB Protein Data Bank. PMID:25183487
Native structure-based modeling and simulation of biomolecular systems per mouse click. PMID:25176255
Uncertainty in integrative structural modeling. PMID:25173450
Human structural proteome-wide characterization of Cyclosporine A targets. PMID:25172926
VASP-E: specificity annotation with a volumetric analysis of electrostatic isopotentials. PMID:25166865
Biological evaluation of potent triclosan-derived inhibitors of the enoyl-acyl carrier protein reductase InhA in drug-sensitive and drug-resistant strains of Mycobacterium tuberculosis. PMID:25165007
Discovery of Sanggenon G as a natural cell-permeable small-molecular weight inhibitor of X-linked inhibitor of apoptosis protein (XIAP). PMID:25161875
PconsFold: improved contact predictions improve protein models. PMID:25161237
ClaRNA: a classifier of contacts in RNA 3D structures based on a comparative analysis of various classification schemes. PMID:25159614
Substituting random forest for multiple linear regression improves binding affinity prediction of scoring functions: Cyscore as a case study. PMID:25159129
Emerging significance of NLRs in inflammatory bowel disease. PMID:25153506
CHARMM additive and polarizable force fields for biophysics and computer-aided drug design. PMID:25149274
Thermal adaptation and clinal mitochondrial DNA variation of European anchovy. PMID:25143035
Dynameomics: data-driven methods and models for utilizing large-scale protein structure repositories for improving fragment-based loop prediction. PMID:25142412
Curation and analysis of multitargeting agents for polypharmacological modeling. PMID:25133604
CHARMM-GUI Membrane Builder toward realistic biological membrane simulations. PMID:25130509
Absence of a simple code: how transcription factors read the genome. PMID:25129887
3,6,2',4',5'-Pentahydroxyflavone, an orally bioavailable multiple protein kinase inhibitor, overcomes gefitinib resistance in non-small cell lung cancer. PMID:25122774
Thermostability of in vitro evolved Bacillus subtilis lipase A: a network and dynamics perspective. PMID:25122499
Local packing density is the main structural determinant of the rate of protein sequence evolution at site level. PMID:25121105
VirtualSpectrum, a tool for simulating peak list for multi-dimensional NMR spectra. PMID:25119482
Anticancer activities of pterostilbene-isothiocyanate conjugate in breast cancer cells: involvement of PPARγ. PMID:25119466
Hydration of protein-RNA recognition sites. PMID:25114050
Fixed-target protein serial microcrystallography with an x-ray free electron laser. PMID:25113598
Chemical interrogation of the malaria kinome. PMID:25111632
A splicing mutation in the novel mitochondrial protein DNAJC11 causes motor neuron pathology associated with cristae disorganization, and lymphoid abnormalities in mice. PMID:25111180
acACS: improving the prediction accuracy of protein subcellular locations and protein classification by incorporating the average chemical shifts composition. PMID:25110749
Design and Synthesis of an Inositol Phosphate Analog Based on Computational Docking Studies. PMID:25110363
Large scale characterization of the LC13 TCR and HLA-B8 structural landscape in reaction to 172 altered peptide ligands: a molecular dynamics simulation study. PMID:25101830
Structural determinants allowing transferase activity in SENSITIVE TO FREEZING 2, classified as a family I glycosyl hydrolase. PMID:25100720
Virtual Screening of compounds to 1-deoxy-Dxylulose 5-phosphate reductoisomerase (DXR) from Plasmodium falciparum. PMID:25097379
Tryparedoxin peroxidase of Leishmania braziliensis: homology modeling and inhibitory effects of flavonoids for anti-leishmanial activity. PMID:25097378
Modular organization and reticulate evolution of the ORF1 of Jockey superfamily transposable elements. PMID:25093042
A crystallographic perspective on sharing data and knowledge. PMID:25091065
AFAL: a web service for profiling amino acids surrounding ligands in proteins. PMID:25085083
Natural product agonists of peroxisome proliferator-activated receptor gamma (PPARγ): a review. PMID:25083916
Exploring representations of protein structure for automated remote homology detection and mapping of protein structure space. PMID:25080993
Template-based C8-SCORPION: a protein 8-state secondary structure prediction method using structural information and context-based features. PMID:25080939
Computational prediction of hinge axes in proteins. PMID:25080829
Structure prediction of polyglutamine disease proteins: comparison of methods. PMID:25080018
Hotspot mutations in KIT receptor differentially modulate its allosterically coupled conformational dynamics: impact on activation and drug sensitivity. PMID:25079768
Structure-based druggability assessment of the mammalian structural proteome with inclusion of light protein flexibility. PMID:25079060
Quantitative method for the assignment of hinge and shear mechanism in protein domain movements. PMID:25078396
MDcons: Intermolecular contact maps as a tool to analyze the interface of protein complexes from molecular dynamics trajectories. PMID:25077693
Analysis and classification of DNA-binding sites in single-stranded and double-stranded DNA-binding proteins using protein information. PMID:25075531
A complete, multi-level conformational clustering of antibody complementarity-determining regions. PMID:25071986
Disjoint combinations profiling (DCP): a new method for the prediction of antibody CDR conformation from sequence. PMID:25071985
Global view of the protein universe. PMID:25071170
Factors affecting the computation of the 13C shielding in disaccharides. PMID:25066622
The Protein Data Bank archive as an open data resource. PMID:25062767
An allosteric modulator of HIV-1 protease shows equipotent inhibition of wild-type and drug-resistant proteases. PMID:25062388
Web-based computational chemistry education with CHARMMing III: Reduction potentials of electron transfer proteins. PMID:25058418
IthaGenes: an interactive database for haemoglobin variations and epidemiology. PMID:25058394
Web-based computational chemistry education with CHARMMing I: Lessons and tutorial. PMID:25057988
Feature-based multiple models improve classification of mutation-induced stability changes. PMID:25057118
In silico comparative characterization of pharmacogenomic missense variants. PMID:25057096
Revision of the classical dopamine D2 agonist pharmacophore based on an integrated medicinal chemistry, homology modelling and computational docking approach. PMID:25056287
From genotype to functional phenotype: unraveling the metabolomic features of colorectal cancer. PMID:25055199
Integrating in silico prediction methods, molecular docking, and molecular dynamics simulation to predict the impact of ALK missense mutations in structural perspective. PMID:25054154
Intermediates in the folding equilibrium of repeat proteins from the TPR family. PMID:25048829
Kinetic and structural characterization of tunnel-perturbing mutants in Bradyrhizobium japonicum proline utilization A. PMID:25046425
Efficient feature selection and classification of protein sequence data in bioinformatics. PMID:25045727
Possible inhibitor from traditional Chinese medicine for the β form of calcium-dependent protein kinase type II in the treatment of major depressive disorder. PMID:25045698
Contribution of each Trp residue toward the intrinsic fluorescence of the Giα1 protein. PMID:25044474
Computational design of protein antigens that interact with the CDR H3 loop of HIV broadly neutralizing antibody 2F5. PMID:25043744
The R-factor gap in macromolecular crystallography: an untapped potential for insights on accurate structures. PMID:25040949
Fast and Accurate Calculation of Protein Depth by Euclidean Distance Transform. PMID:25035865
In silico designing and molecular docking of a potent analog against Staphylococcus aureus porphobilinogen synthase. PMID:25035635
The mitochondrial and chloroplast genomes of the haptophyte Chrysochromulina tobin contain unique repeat structures and gene profiles. PMID:25034814
Evolutionary relationship of disease resistance genes in soybean and Arabidopsis specific for the Pseudomonas syringae effectors AvrB and AvrRpm1. PMID:25034017
Stability curve prediction of homologous proteins using temperature-dependent statistical potentials. PMID:25032839
LipidWrapper: an algorithm for generating large-scale membrane models of arbitrary geometry. PMID:25032790
A performance/cost evaluation for a GPU-based drug discovery application on volunteer computing. PMID:25025055
A unified coarse-grained model of biological macromolecules based on mean-field multipole-multipole interactions. PMID:25024008
Thermodynamics of Water in an Enzyme Active Site: Grid-Based Hydration Analysis of Coagulation Factor Xa. PMID:25018673
Ugi 4-CR Synthesis of γ- and δ-Lactams providing new access to diverse enzyme interactions, a PDB analysis. PMID:25013719
Inhibition of human dyskerin as a new approach to target ribosome biogenesis. PMID:25010840
Crystallization screening: the influence of history on current practice. PMID:25005076
A phylogenetic analysis of the ubiquitin superfamily based on sequence and structural information. PMID:24997693
PCASSO: a fast and efficient Cα-based method for accurately assigning protein secondary structure elements. PMID:24995959
Analysis of stacking overlap in nucleic acid structures: algorithm and application. PMID:24990628
Solution NMR structures of immunoglobulin-like domains 7 and 12 from obscurin-like protein 1 contribute to the structural coverage of the Human Cancer Protein Interaction Network. PMID:24989974
Statistical analysis of crystallization database links protein physico-chemical features with crystallization mechanisms. PMID:24988076
Investigation of the flexibility of protein kinases implicated in the pathology of Alzheimer's disease. PMID:24983862
New technologies in computer-aided drug design: Toward target identification and new chemical entity discovery. PMID:24980533
Differential global structural changes in the core particle of yeast and mouse proteasome induced by ligand binding. PMID:24979800
enDNA-Prot: identification of DNA-binding proteins by applying ensemble learning. PMID:24977146
Docking server for the identification of heparin binding sites on proteins. PMID:24974889
Reconstructing protein structures by neural network pairwise interaction fields and iterative decoy set construction. PMID:24970210
Quantum mechanical modeling: a tool for the understanding of enzyme reactions. PMID:24970187
Evaluation of novel Saquinavir analogs for resistance mutation compatibility and potential as an HIV-Protease inhibitor drug. PMID:24966525
Testing the sensitivities of noncognate inhibitors to varicella zoster virus thymidine kinase: implications for postherpetic neuralgia therapy with existing agents. PMID:24961898
Ligand-based pharmacophore modeling and virtual screening for the discovery of novel 17β-hydroxysteroid dehydrogenase 2 inhibitors. PMID:24960438
Finding semirigid domains in biomolecules by clustering pair-distance variations. PMID:24959586
iDrug: a web-accessible and interactive drug discovery and design platform. PMID:24955134
Polymorphic Protein Crystal Growth: Influence of Hydration and Ions in Glucose Isomerase. PMID:24955067
Structure-based characterization of multiprotein complexes. PMID:24954616
Exploring the structural and functional impact of the ALK F1174L mutation using bioinformatics approach. PMID:24952065
The emerging era of genomic data integration for analyzing splice isoform function. PMID:24951248
Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery. PMID:24950326
IIS--Integrated Interactome System: a web-based platform for the annotation, analysis and visualization of protein-metabolite-gene-drug interactions by integrating a variety of data sources and tools. PMID:24949626
Solution NMR structures of homeodomains from human proteins ALX4, ZHX1, and CASP8AP2 contribute to the structural coverage of the Human Cancer Protein Interaction Network. PMID:24941917
Evidence of extensive DNA transfer between bacteroidales species within the human gut. PMID:24939888
Nanoinformatics knowledge infrastructures: bringing efficient information management to nanomedical research. PMID:24932210
Coverage of protein domain families with structural protein-protein interactions: current progress and future trends. PMID:24931138
Cloud4Psi: cloud computing for 3D protein structure similarity searching. PMID:24930141
Functional evolution of PLP-dependent enzymes based on active-site structural similarities. PMID:24920327
Automation in biological crystallization. PMID:24915074
Computational evaluation of factors governing catalytic 2-keto acid decarboxylation. PMID:24912593
MOPED 2.5--an integrated multi-omics resource: multi-omics profiling expression database now includes transcriptomics data. PMID:24910945
Scoring docking conformations using predicted protein interfaces. PMID:24906633
Concentration dependent viscosity of monoclonal antibody solutions: explaining experimental behavior in terms of molecular properties. PMID:24906598
Profiling the orphan enzymes. PMID:24906382
Primary sequence contribution to the optical function of the eye lens. PMID:24903231
Discovery of AZD8931, an Equipotent, Reversible Inhibitor of Signaling by EGFR, HER2, and HER3 Receptors. PMID:24900741
Design and synthesis of potent, selective inhibitors of matriptase. PMID:24900505
Bivalent Ligands for the Serotonin 5-HT3 Receptor. PMID:24900351
Drawing the PDB: Protein-Ligand Complexes in Two Dimensions. PMID:24900245
Hydration Site Thermodynamics Explain SARs for Triazolylpurines Analogues Binding to the A2A Receptor. PMID:24900189
The Purine Bias of Coding Sequences is Determined by Physicochemical Constraints on Proteins. PMID:24899802
Pharmacoinformatics elucidation of potential drug targets against migraine to target ion channel protein KCNK18. PMID:24899801
Predicted structure and domain organization of rotavirus capping enzyme and innate immune antagonist VP3. PMID:24899176
Structure of the BTB domain of Keap1 and its interaction with the triterpenoid antagonist CDDO. PMID:24896564
Probing the average local structure of biomolecules using small-angle scattering and scaling laws. PMID:24896127
Kv1.3 channel-blocking immunomodulatory peptides from parasitic worms: implications for autoimmune diseases. PMID:24891519
Conformation-dependent backbone geometry restraints set a new standard for protein crystallographic refinement. PMID:24890778
The structural and functional signatures of proteins that undergo multiple events of post-translational modification. PMID:24888500
The HIVToolbox 2 web system integrates sequence, structure, function and mutation analysis. PMID:24886930
Combination of 2D/3D ligand-based similarity search in rapid virtual screening from multimillion compound repositories. Selection and biological evaluation of potential PDE4 and PDE5 inhibitors. PMID:24879613
Prediction and redesign of protein-protein interactions. PMID:24878423
Role of calcium signaling in the transcriptional regulation of the apicoplast genome of Plasmodium falciparum. PMID:24877144
Predicting enzyme adsorption to lignin films by calculating enzyme surface hydrophobicity. PMID:24876380
Inhibition of dihydroceramide desaturase activity by the sphingosine kinase inhibitor SKI II. PMID:24875537
DDI-CPI, a server that predicts drug-drug interactions through implementing the chemical-protein interactome. PMID:24875476
Exploration of the dynamic properties of protein complexes predicted from spatially constrained protein-protein interaction networks. PMID:24874694
Anatomy of β-strands at protein-protein interfaces. PMID:24870802
Extensive expansion of A1 family aspartic proteinases in fungi revealed by evolutionary analyses of 107 complete eukaryotic proteomes. PMID:24869856
The interaction pattern between a homology model of 40S ribosomal S9 protein of Rhizoctonia solani and 1-hydroxyphenaize by docking study. PMID:24864254
Enhancing UCSF Chimera through web services. PMID:24861624
SSpro/ACCpro 5: almost perfect prediction of protein secondary structure and relative solvent accessibility using profiles, machine learning and structural similarity. PMID:24860169
Structural probing of off-target G protein-coupled receptor activities within a series of adenosine/adenine congeners. PMID:24859150
PTM-SD: a database of structurally resolved and annotated posttranslational modifications in proteins. PMID:24857970
Molecular modelling study of the PPARγ receptor in relation to the mode of action/adverse outcome pathway framework for liver steatosis. PMID:24857909
Enrichment of chemical libraries docked to protein conformational ensembles and application to aldehyde dehydrogenase 2. PMID:24856086
The amyloid state and its association with protein misfolding diseases. PMID:24854788
LocTree3 prediction of localization. PMID:24848019
RNABindRPlus: a predictor that combines machine learning and sequence homology-based methods to improve the reliability of predicted RNA-binding residues in proteins. PMID:24846307
Protonated form: the potent form of potassium-competitive acid blockers. PMID:24845980
(+)-2-(1-Hydroxyl-4-oxocyclohexyl) ethyl caffeate suppresses solar UV-induced skin carcinogenesis by targeting PI3K, ERK1/2, and p38. PMID:24845061
A New Distributed Algorithm for Side-Chain Positioning in the Process of Protein Docking*. PMID:24844567
Tetra- and pentacyclic triterpene acids from the ancient anti-inflammatory remedy frankincense as inhibitors of microsomal prostaglandin E(2) synthase-1. PMID:24844534
ProTox: a web server for the in silico prediction of rodent oral toxicity. PMID:24838562
RASS: a web server for RNA alignment in the joint sequence-structure space. PMID:24831547
AIDA: ab initio domain assembly server. PMID:24831546
Protein-protein interface detection using the energy centrality relationship (ECR) characteristic of proteins. PMID:24830938
Flexible Refinement of Protein-Ligand Docking on Manifolds. PMID:24830567
PRISM: a web server and repository for prediction of protein-protein interactions and modeling their 3D complexes. PMID:24829450
Differential effects of CSF-1R D802V and KIT D816V homologous mutations on receptor tertiary structure and allosteric communication. PMID:24828813
Mutatomics analysis of the systematic thermostability profile of Bacillus subtilis lipase A. PMID:24827611
Modeling of a new tubercular maltosyl transferase, GlgE, study of its binding sites and virtual screening. PMID:24820953
Evolution of tertiary structure of viral RNA dependent polymerases. PMID:24816789
Probing the global and local dynamics of aminoacyl-tRNA synthetases using all-atom and coarse-grained simulations. PMID:24810463
Alpha-bulges in G protein-coupled receptors. PMID:24806342
Influence of the length and positioning of the antiestrogenic side chain of endoxifen and 4-hydroxytamoxifen on gene activation and growth of estrogen receptor positive cancer cells. PMID:24805199
Predicting the Impact of Missense Mutations on Protein-Protein Binding Affinity. PMID:24803870
SymD webserver: a platform for detecting internally symmetric protein structures. PMID:24799435
PredictProtein--an open resource for online prediction of protein structural and functional features. PMID:24799431
Molecular dynamics, dynamic site mapping, and highthroughput virtual screening on leptin and the Ob receptor as anti-obesity target. PMID:24797089
Characterization of the geometry and topology of DNA pictured as a discrete collection of atoms. PMID:24791158
High-quality NMR structure of human anti-apoptotic protein domain Mcl-1(171-327) for cancer drug design. PMID:24789074
The relationships between XPC binding to conformationally diverse DNA adducts and their excision by the human NER system: is there a correlation? PMID:24784728
TSpred: a web server for the rational design of temperature-sensitive mutants. PMID:24782523
NEP: web server for epitope prediction based on antibody neutralization of viral strains with diverse sequences. PMID:24782517
Arsenic and cadmium are inhibitors of cyanobacterial dinitrogenase reductase (nifH1) gene. PMID:24781142
Heteroaromatic π-stacking energy landscapes. PMID:24773380
RNApdbee--a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs. PMID:24771339
Assembly of nonheme Mn/Fe active sites in heterodinuclear metalloproteins. PMID:24771036
The major cockroach allergen Bla g 4 binds tyramine and octopamine. PMID:24769496
A New Approach to Rigid Body Minimization with Application to Molecular Docking. PMID:24763338
Knowledge-based fragment binding prediction. PMID:24762971
Genome-wide analysis of the bZIP transcription factors in cucumber. PMID:24760072
Large-scale determination of sequence, structure, and function relationships in cytosolic glutathione transferases across the biosphere. PMID:24756107
Genetic and pharmacological strategies to refunctionalize the von Hippel Lindau R167Q mutant protein. PMID:24755468
Improving B-cell epitope prediction and its application to global antibody-antigen docking. PMID:24753488
AlignMe--a membrane protein sequence alignment web server. PMID:24753425
An automated framework for NMR resonance assignment through simultaneous slice picking and spin system forming. PMID:24748536
A critical evaluation of in silico methods for detection of membrane protein intrinsic disorder. PMID:24739163
Training-free atomistic prediction of nucleosome occupancy. PMID:24733939
New insights into Dehalococcoides mccartyi metabolism from a reconstructed metabolic network-based systems-level analysis of D. mccartyi transcriptomes. PMID:24733489
Intermolecular β-strand networks avoid hub residues and favor low interconnectedness: a potential protection mechanism against chain dissociation upon mutation. PMID:24733378
Application of Hybrid Functional Groups to Predict ATP Binding Proteins. PMID:24729962
Extension of UNRES force field to treat polypeptide chains with D-amino-acid residues. PMID:24729761
The DynaMine webserver: predicting protein dynamics from sequence. PMID:24728994
C(α) torsion angles as a flexible criterion to extract secrets from a molecular dynamics simulation. PMID:24728650
Redefining the PF06864 Pfam family based on Burkholderia pseudomallei PilO2(Bp) S-SAD crystal structure. PMID:24728008
Use of long term molecular dynamics simulation in predicting cancer associated SNPs. PMID:24722014
Mechanistic and bioinformatic investigation of a conserved active site helix in α-isopropylmalate synthase from Mycobacterium tuberculosis, a member of the DRE-TIM metallolyase superfamily. PMID:24720347
Interaction of 6 mercaptopurine with calf thymus DNA--deciphering the binding mode and photoinduced DNA damage. PMID:24718609
A tractable genotype-phenotype map modelling the self-assembly of protein quaternary structure. PMID:24718456
Encounter complexes and dimensionality reduction in protein-protein association. PMID:24714491
Biochemical properties of ectoine hydroxylases from extremophiles and their wider taxonomic distribution among microorganisms. PMID:24714029
Conformational Changes of Congenital FVII Variants with Defective Binding to Tissue Factor ARG304GLN (FVII Padua), ARG 304TRP (FVII Nagoya) and ARG79GLN (FVII Shinjo or Tondabayashi). PMID:24711753
The landscape of somatic mutations in epigenetic regulators across 1,000 paediatric cancer genomes. PMID:24710217
Protein structure determination by MicroED. PMID:24709395
Interactions outside the proteinase-binding loop contribute significantly to the inhibition of activated coagulation factor XII by its canonical inhibitor from corn. PMID:24706752
Eupafolin suppresses prostate cancer by targeting phosphatidylinositol 3-kinase-mediated Akt signaling. PMID:24700667
The histone-fold complex MHF is remodeled by FANCM to recognize branched DNA and protect genome stability. PMID:24699063
A brief history of macromolecular crystallography, illustrated by a family tree and its Nobel fruits. PMID:24698025
Evidence of positive selection in mitochondrial complexes I and V of the African elephant. PMID:24695069
Protoss: a holistic approach to predict tautomers and protonation states in protein-ligand complexes. PMID:24694216
A structure-based model for predicting serum albumin binding. PMID:24691448
FragBuilder: an efficient Python library to setup quantum chemistry calculations on peptides models. PMID:24688855
Measuring the shapes of macromolecules - and why it matters. PMID:24688748
Inverted topologies in membrane proteins: a mini-review. PMID:24688744
Frequency of dipeptides and antidipeptides. PMID:24688741
Membrane Packing Problems: A short Review on computational Membrane Modeling Methods and Tools. PMID:24688707
A frequency-based linguistic approach to protein decoding and design: Simple concepts, diverse applications, and the SCS Package. PMID:24688703
Computational tools for rational protein engineering of aldolases. PMID:24688657
Thumb-loops up for catalysis: a structure/function investigation of a functional loop movement in a GH11 xylanase. PMID:24688637
Lassomycin, a ribosomally synthesized cyclic peptide, kills mycobacterium tuberculosis by targeting the ATP-dependent protease ClpC1P1P2. PMID:24684906
Using DelPhi capabilities to mimic protein's conformational reorganization with amino acid specific dielectric constants. PMID:24683422
Topology Based Selection and Curation of Level Sets. PMID:24683389
Automated procedure for contact-map-based protein structure reconstruction. PMID:24682239
Systematic detection of internal symmetry in proteins using CE-Symm. PMID:24681267
Prediction and analysis of surface hydrophobic residues in tertiary structure of proteins. PMID:24672404
Force field independent metal parameters using a nonbonded dummy model. PMID:24670003
A graph theoretic approach to utilizing protein structure to identify non-random somatic mutations. PMID:24669769
FreeContact: fast and free software for protein contact prediction from residue co-evolution. PMID:24669753
In-silico analysis of binding site features and substrate selectivity in plant flavonoid-3-O glycosyltransferases (F3GT) through molecular modeling, docking and dynamics simulation studies. PMID:24667893
Fast and accurate multivariate Gaussian modeling of protein families: predicting residue contacts and protein-interaction partners. PMID:24663061
Randomly organized lipids and marginally stable proteins: a coupling of weak interactions to optimize membrane signaling. PMID:24657395
Bayesian energy landscape tilting: towards concordant models of molecular ensembles. PMID:24655513
Inhibition of STAT3 dimerization and acetylation by garcinol suppresses the growth of human hepatocellular carcinoma in vitro and in vivo. PMID:24655440
Identification of novel potential antibiotics against Staphylococcus using structure-based drug screening targeting dihydrofolate reductase. PMID:24655350
Engineering and characterizing monomeric fluorescent proteins for live-cell imaging applications. PMID:24651502
Theoretical and experimental studies of new modified isoflavonoids as potential inhibitors of topoisomerase I from Plasmodium falciparum. PMID:24651068
Fast protein folding kinetics. PMID:24641816
BD SIMULATIONS OF THE IONIC STRENGTH DEPENDENCE OF THE INTERACTIONS BETWEEN TRIOSE PHOSPHATE ISOMERASE AND F-ACTIN. PMID:24639622
Detection, characterization and evolution of internal repeats in Chitinases of known 3-D structure. PMID:24637574
A novel chimeric avidin with increased thermal stability using DNA shuffling. PMID:24632863
High precision prediction of functional sites in protein structures. PMID:24632601
Atomic basis of CRM1-cargo recognition, release and inhibition. PMID:24631835
Natural polymorphisms and unusual mutations in HIV-1 protease with potential antiretroviral resistance: a bioinformatic analysis. PMID:24629078
Canonical structures of short CDR-L3 in antibodies. PMID:24623659
Virtual Screening of Indonesian Herbal Database as HIV-1 Protease Inhibitor. PMID:24616554
Mechanistic studies of the biogenesis and folding of outer membrane proteins in vitro and in vivo: what have we learned to date? PMID:24613287
Metal oxide based multisensor array and portable database for field analysis of antioxidants. PMID:24610993
Defining the conformation of the estrogen receptor complex that controls estrogen-induced apoptosis in breast cancer. PMID:24608856
Molecular analysis of the interaction between staphylococcal virulence factor Sbi-IV and complement C3d. PMID:24606940
A flexible docking scheme efficiently captures the energetics of glycan-cyanovirin binding. PMID:24606938
Structural insights into E. coli porphobilinogen deaminase during synthesis and exit of 1-hydroxymethylbilane. PMID:24603363
Elucidating common structural features of human pathogenic variations using large-scale atomic-resolution protein networks. PMID:24599843
Experimental and computational mutagenesis to investigate the positioning of a general base within an enzyme active site. PMID:24597914
Identification of isosilybin a from milk thistle seeds as an agonist of peroxisome proliferator-activated receptor gamma. PMID:24597776
Does the cis/trans configuration of peptide bonds in bioactive tripeptides play a role in ACE-1 enzyme inhibition? PMID:24596454
Data management in the modern structural biology and biomedical research environment. PMID:24590705
Hepatitis C virus genetic variability and the presence of NS5B resistance-associated mutations as natural polymorphisms in selected genotypes could affect the response to NS5B inhibitors. PMID:24590484
iLIR: A web resource for prediction of Atg8-family interacting proteins. PMID:24589857
ENZYMAP: exploiting protein annotation for modeling and predicting EC number changes in UniProt/Swiss-Prot. PMID:24586563
Population structure and evolution of Rhinoviruses. PMID:24586469
Sensor domain of histidine kinase KinB of Pseudomonas: a helix-swapped dimer. PMID:24573685
Minimal model of self-assembly: emergence of diversity and complexity. PMID:24571643
Large-scale analysis of B-cell epitopes on influenza virus hemagglutinin - implications for cross-reactivity of neutralizing antibodies. PMID:24570677
Chemogenomics knowledgebased polypharmacology analyses of drug abuse related G-protein coupled receptors and their ligands. PMID:24567719
Functional properties of a cysteine proteinase from pineapple fruit with improved resistance to fungal pathogens in Arabidopsis thaliana. PMID:24566309
Genes associated with genotype-specific DNA methylation in squamous cell carcinoma as candidate drug targets. PMID:24565165
An effective and effecient peptide binding prediction approach for a broad set of HLA-DR molecules based on ordered weighted averaging of binding pocket profiles. PMID:24565049
The role of electrostatic energy in prediction of obligate protein-protein interactions. PMID:24564955
DINC: a new AutoDock-based protocol for docking large ligands. PMID:24564952
An aggregate analysis of many predicted structures to reduce errors in protein structure comparison caused by conformational flexibility. PMID:24564934
Prediction of protein interaction types based on sequence and network features. PMID:24564924
HopDock: a probabilistic search algorithm for decoy sampling in protein-protein docking. PMID:24564839
Genome-wide structural modelling of TCR-pMHC interactions. PMID:24564684
Cluster based prediction of PDZ-peptide interactions. PMID:24564547
Incorporating substrate sequence motifs and spatial amino acid composition to identify kinase-specific phosphorylation sites on protein three-dimensional structures. PMID:24564522
Proposing a highly accurate protein structural class predictor using segmentation-based features. PMID:24564476
Structural analysis on mutation residues and interfacial water molecules for human TIM disease understanding. PMID:24564410
Context-based preprocessing of molecular docking data. PMID:24564276
The binary protein-protein interaction landscape of Escherichia coli. PMID:24561554
A key n→π* Interaction in N-acyl homoserine lactones. PMID:24556113
Advancing the activity cliff concept. PMID:24555097
Prospective virtual screening for novel p53-MDM2 inhibitors using ultrafast shape recognition. PMID:24554192
Determining the Role of the Aromatic Ring of N-Arylmethyl ent-conduramine F-1 in their Interactions with α-Glucosidases by Saturation Transfer Difference NMR Spectroscopy Experiments. PMID:24551486
Functions and regulation of quorum-sensing in Agrobacterium tumefaciens. PMID:24550924
Curcumin suppresses proliferation of colon cancer cells by targeting CDK2. PMID:24550143
Steered molecular dynamics identifies critical residues of the Nodamura virus B2 suppressor of RNAi. PMID:24549790
Weak data do not make a free lunch, only a cheap meal. PMID:24531460
C-H…pi interactions in proteins: prevalence, pattern of occurrence, residue propensities, location, and contribution to protein stability. PMID:24526385
Evaluating the stability of disulfide bridges in proteins: a torsional potential energy surface for diethyl disulfide. PMID:24523568
Anti-arthritis effects of (E)-2,4-bis(p-hydroxyphenyl)-2-butenal are mediated by inhibition of the STAT3 pathway. PMID:24520814
Blind prediction performance of RosettaAntibody 3.0: grafting, relaxation, kinematic loop modeling, and full CDR optimization. PMID:24519881
Enhancing the quality of protein conformation ensembles with relative populations. PMID:24519023
PPS: A computing engine to find Palindromes in all Protein sequences. PMID:24516327
In silico analysis of Myoglobin in Channa striata. PMID:24516321
Computational large-scale mapping of protein-protein interactions using structural complexes. PMID:24510594
Discovery of new liver X receptor agonists by pharmacophore modeling and shape-based virtual screening. PMID:24502802
Sequence dependent variations in RNA duplex are related to non-canonical hydrogen bond interactions in dinucleotide steps. PMID:24502340
Structural interface parameters are discriminatory in recognising near-native poses of protein-protein interactions. PMID:24498255
Variation of human immunodeficiency virus type-1 reverse transcriptase within the simian immunodeficiency virus genome of RT-SHIV. PMID:24498008
Virtual screening with AutoDock Vina and the common pharmacophore engine of a low diversity library of fragments and hits against the three allosteric sites of HIV integrase: participation in the SAMPL4 protein-ligand binding challenge. PMID:24493410
Combinatorial approach for large-scale identification of linked peptides from tandem mass spectrometry spectra. PMID:24493012
Improving predictions of protein-protein interfaces by combining amino acid-specific classifiers based on structural and physicochemical descriptors with their weighted neighbor averages. PMID:24489849
Forcefield_PTM: Ab Initio Charge and AMBER Forcefield Parameters for Frequently Occurring Post-Translational Modifications. PMID:24489522
Multi-algorithm and multi-model based drug target prediction and web server. PMID:24487966
Parallel implementation of 3D protein structure similarity searches using a GPU and the CUDA. PMID:24481593
Testing and validation of the Automated Topology Builder (ATB) version 2.0: prediction of hydration free enthalpies. PMID:24477799
A knowledge-based scoring function for protein-RNA interactions derived from a statistical mechanics-based iterative method. PMID:24476917
Affinity improvement of a therapeutic antibody by structure-based computational design: generation of electrostatic interactions in the transition state stabilizes the antibody-antigen complex. PMID:24475232
Non-redundant unique interface structures as templates for modeling protein interactions. PMID:24475173
Sequence based prediction of DNA-binding proteins based on hybrid feature selection using random forest and Gaussian naïve Bayes. PMID:24475169
Linker-extended native cyanovirin-N facilitates PEGylation and potently inhibits HIV-1 by targeting the glycan ligand. PMID:24475123
istar: a web platform for large-scale protein-ligand docking. PMID:24475049
Crystal structure of carbapenemase OXA-58 from Acinetobacter baumannii. PMID:24468777
Dynafold: a dynamic programming approach to protein backbone structure determination from minimal sets of Residual Dipolar Couplings. PMID:24467760
Elucidation of the molecular mechanism and the efficacy in vivo of a novel 1,4-benzoquinone that inhibits 5-lipoxygenase. PMID:24467325
Genome-wide investigation and expression analyses of WD40 protein family in the model plant foxtail millet (Setaria italica L.). PMID:24466268
Structural Consequences of Chromophore Formation and Exploration of Conserved Lid Residues amongst Naturally Occurring Fluorescent Proteins. PMID:24465077
Cation-π interactions of methylated ammonium ions: a quantum mechanical study. PMID:24464782
Quantitative characterization of protein tertiary motifs. PMID:24464316
Assessment of physical stability of an antibody drug conjugate by higher order structure analysis: impact of thiol- maleimide chemistry. PMID:24464270
Virtual screening of the SAMPL4 blinded HIV integrase inhibitors dataset. PMID:24458507
GeneSV - an Approach to Help Characterize Possible Variations in Genomic and Protein Sequences. PMID:24453480
Carboxylic acids in crystallization of macromolecules: learning from successful crystallization experiments. PMID:24452510
Converting the yeast arginine can1 permease to a lysine permease. PMID:24448798
Predicting DNA-binding sites of proteins based on sequential and 3D structural information. PMID:24448651
Modeling protein assemblies in the proteome. PMID:24445405
RASP: rapid and robust backbone chemical shift assignments from protein structure. PMID:24445369
Joint probabilistic-logical refinement of multiple protein feature predictors. PMID:24428894
The isolated carboxy-terminal domain of human mitochondrial leucyl-tRNA synthetase rescues the pathological phenotype of mitochondrial tRNA mutations in human cells. PMID:24413190
PeptiSite: a structural database of peptide binding sites in 4D. PMID:24406170
Discovery of novel inhibitors of HIV-1 reverse transcriptase through virtual screening of experimental and theoretical ensembles. PMID:24405985
Validating computer simulations of enantioselective catalysis; reproducing the large steric and entropic contributions in Candida Antarctica lipase B. PMID:24403025
Charge segregation and low hydrophobicity are key features of ribosomal proteins from different organisms. PMID:24398678
Protein structure refinement of CASP target proteins using GNEIMO torsional dynamics method. PMID:24397429
Decline in serum cholinesterase activities predicts 2-year major adverse cardiac events. PMID:24395570
In silico analysis of the conservation of human toxicity and endocrine disruption targets in aquatic species. PMID:24392850
Protein NMR structures refined with Rosetta have higher accuracy relative to corresponding X-ray crystal structures. PMID:24392845
Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics. PMID:24391900
Redox specificity of 2-hydroxyacid-coupled NAD(+)/NADH dehydrogenases: a study exploiting "reactive" arginine as a reporter of protein electrostatics. PMID:24391777
PT19c, Another Nonhypercalcemic Vitamin D2 Derivative, Demonstrates Antitumor Efficacy in Epithelial Ovarian and Endometrial Cancer Models. PMID:24386512
BP-Dock: a flexible docking scheme for exploring protein-ligand interactions based on unbound structures. PMID:24380381
Optimization of an AMBER force field for the artificial nucleic acid, LNA, and benchmarking with NMR of L(CAAU). PMID:24377321
Signatures of n→π* interactions in proteins. PMID:24375625
Scaffold mining of kinase hinge binders in crystal structure database. PMID:24375079
Conformation and stability of intramolecular telomeric G-quadruplexes: sequence effects in the loops. PMID:24367632
A conformational restriction in the influenza A virus neuraminidase binding site by R152 results in a combinational effect of I222T and H274Y on oseltamivir resistance. PMID:24366752
A structural biology approach enables the development of antimicrobials targeting bacterial immunophilins. PMID:24366729
Dihedral-based segment identification and classification of biopolymers I: proteins. PMID:24364820
The marine cyanobacterial metabolite gallinamide A is a potent and selective inhibitor of human cathepsin L. PMID:24364476
Dihedral-based segment identification and classification of biopolymers II: polynucleotides. PMID:24364355
Cube - an online tool for comparison and contrasting of protein sequences. PMID:24363790
Protein structural ensembles are revealed by redefining X-ray electron density noise. PMID:24363322
Interaction-based discovery of functionally important genes in cancers. PMID:24362839
Structural basis for the design of selective phosphodiesterase 4B inhibitors. PMID:24361374
On the intrinsic disorder status of the major players in programmed cell death pathways. PMID:24358900
On the encoding of proteins for disordered regions prediction. PMID:24358161
Validation of metal-binding sites in macromolecular structures with the CheckMyMetal web server. PMID:24356774
In vitro evaluation of novel inhibitors against the NS2B-NS3 protease of dengue fever virus type 4. PMID:24352016
Probabilistic grammatical model for helix-helix contact site classification. PMID:24350601
Amino acid changes in disease-associated variants differ radically from variants observed in the 1000 genomes project dataset. PMID:24348229
Improving structural similarity based virtual screening using background knowledge. PMID:24341870
Applying physics-based scoring to calculate free energies of binding for single amino acid mutations in protein-protein complexes. PMID:24340062
Sequence-based Gaussian network model for protein dynamics. PMID:24336646
Molecular insights into the recognition of N-terminal histone modifications by the BRPF1 bromodomain. PMID:24333487
Generating NMR chemical shift assignments of intrinsically disordered proteins using carbon-detected NMR methods. PMID:24333248
BioSuper: a web tool for the superimposition of biomolecules and assemblies with rotational symmetry. PMID:24330655
Molecular evolution of threonine dehydratase in bacteria. PMID:24324624
Transcriptional protein-protein cooperativity in POU/HMG/DNA complexes revealed by normal mode analysis. PMID:24324527
Exploring the "dark matter" of a mammalian proteome by protein structure and function modeling. PMID:24321360
Studies of the interaction between isoimperatorin and human serum albumin by multispectroscopic method: identification of possible binding site of the compound using esterase activity of the protein. PMID:24319355
The critical role of the loops of triosephosphate isomerase for its oligomerization, dynamics, and functionality. PMID:24318986
Quantifying reproducibility in computational biology: the case of the tuberculosis drugome. PMID:24312207
Flavonoid from Carica papaya inhibits NS2B-NS3 protease and prevents Dengue 2 viral assembly. PMID:24307765
SCOPe: Structural Classification of Proteins--extended, integrating SCOP and ASTRAL data and classification of new structures. PMID:24304899
Detecting protein candidate fragments using a structural alphabet profile comparison approach. PMID:24303019
Coevolutionary signals across protein lineages help capture multiple protein conformations. PMID:24297889
ASD v2.0: updated content and novel features focusing on allosteric regulation. PMID:24293647
Chemical annotation of small and peptide-like molecules at the Protein Data Bank. PMID:24291661
Ribonucleotides as nucleotide excision repair substrates. PMID:24290807
Predicting drug-target interactions using probabilistic matrix factorization. PMID:24289468
PDBe: Protein Data Bank in Europe. PMID:24288376
PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools. PMID:24285306
Lysine and arginine content of proteins: computational analysis suggests a new tool for solubility design. PMID:24283752
[6]-shogaol inhibits growth and induces apoptosis of non-small cell lung cancer cells by directly regulating Akt1/2. PMID:24282290
Introducing glycomics data into the Semantic Web. PMID:24280648
Imatinib analogs as potential agents for PET imaging of Bcr-Abl and c-KIT expression at a kinase level. PMID:24280068
Interface dynamics explain assembly dependency of influenza neuraminidase catalytic activity. PMID:24279589
Integrating structure to protein-protein interaction networks that drive metastasis to brain and lung in breast cancer. PMID:24278371
Exploring the composition of protein-ligand binding sites on a large scale. PMID:24277997
Soluble expression of proteins correlates with a lack of positively-charged surface. PMID:24276756
In-silico screening of cancer associated mutation on PLK1 protein and its structural consequences. PMID:24271645
Heme-bound nitroxyl, hydroxylamine, and ammonia ligands as intermediates in the reaction cycle of cytochrome c nitrite reductase: a theoretical study. PMID:24271207
Prediction of Intrinsic Disorder in MERS-CoV/HCoV-EMC Supports a High Oral-Fecal Transmission. PMID:24270586
Protein folding and de novo protein design for biotechnological applications. PMID:24268901
Sequence and structure based models of HIV-1 protease and reverse transcriptase drug resistance. PMID:24268064
HPDB-Haskell library for processing atomic biomolecular structures in Protein Data Bank format. PMID:24267035
ArchDB 2014: structural classification of loops in proteins. PMID:24265221
Classification of domain movements in proteins using dynamic contact graphs. PMID:24260562
Interplay of hydrogen bonds and n→π* interactions in proteins. PMID:24256417
β-lactoglobulin's conformational requirements for ligand binding at the calyx and the dimer interphase: a flexible docking study. PMID:24255705
Efficient Computation of Small-Molecule Configurational Binding Entropy and Free Energy Changes by Ensemble Enumeration. PMID:24250277
Inclusion of multiple fragment types in the site identification by ligand competitive saturation (SILCS) approach. PMID:24245913
Functional interpretation of a non-gut hemocoelic tissue aminopeptidase N (APN) in a lepidopteran insect pest Achaea janata. PMID:24244508
Structure-activity relationships of constrained phenylethylamine ligands for the serotonin 5-HT2 receptors. PMID:24244317
Structure-based function prediction of uncharacterized protein using binding sites comparison. PMID:24244144
Computational protein design quantifies structural constraints on amino acid covariation. PMID:24244128
The Reactome pathway knowledgebase. PMID:24243840
Structural updates of alignment of protein domains and consequences on evolutionary models of domain superfamilies. PMID:24237883
The IUPHAR/BPS Guide to PHARMACOLOGY: an expert-driven knowledgebase of drug targets and their ligands. PMID:24234439
In silico modeling and functional interpretations of Cry1Ab15 toxin from Bacillus thuringiensis BtB-Hm-16. PMID:24228249
Inclusion of the orientational entropic effect and low-resolution experimental information for protein-protein docking in Critical Assessment of PRedicted Interactions (CAPRI). PMID:24227686
Structure-activity relationships of peptidomimetics that inhibit PPI of HER2-HER3. PMID:24222531
Episodes of horizontal gene-transfer and gene-fusion led to co-existence of different metal-ion specific glyoxalase I. PMID:24220130
Packing interface energetics in different crystal forms of the λ Cro dimer. PMID:24218107
SAbDab: the structural antibody database. PMID:24214988
A structure-guided approach for protein pocket modeling and affinity prediction. PMID:24214361
Electrophilic fatty acid species inhibit 5-lipoxygenase and attenuate sepsis-induced pulmonary inflammation. PMID:24206143
Classification of α-helical membrane proteins using predicted helix architectures. PMID:24204844
Zebavidin--an avidin-like protein from zebrafish. PMID:24204770
A comprehensive survey of small-molecule binding pockets in proteins. PMID:24204237
The quality and validation of structures from structural genomics. PMID:24203341
High-resolution network biology: connecting sequence with function. PMID:24197012
An accurate method for prediction of protein-ligand binding site on protein surface using SVM and statistical depth function. PMID:24195070
JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles. PMID:24194598
LenVarDB: database of length-variant protein domains. PMID:24194591
Model morphing and sequence assignment after molecular replacement. PMID:24189236
Evolutionary analysis of hydrophobin gene family in two wood-degrading basidiomycetes, Phlebia brevispora and Heterobasidion annosum s.l. PMID:24188142
Functional conservation of HIV-1 Gag: implications for rational drug design. PMID:24176092
Structure-based barcoding of proteins. PMID:24170674
Protein signatures using electrostatic molecular surfaces in harmonic space. PMID:24167780
Protein function annotation by local binding site surface similarity. PMID:24166661
A comparative study of ribosomal proteins: linkage between amino acid distribution and ribosomal assembly. PMID:24152303
Exploring the Trypanosoma brucei Hsp83 potential as a target for structure guided drug design. PMID:24147171
Molecular dynamic simulation reveals damaging impact of RAC1 F28L mutation in the switch I region. PMID:24146998
Dolutegravir interactions with HIV-1 integrase-DNA: structural rationale for drug resistance and dissociation kinetics. PMID:24146996
Confidence-guided local structure prediction with HHfrag. PMID:24146881
Identification and structural-functional analysis of cyclin-dependent kinases of the cattle tick Rhipicephalus (Boophilus) microplus. PMID:24146826
On the role of aggregation prone regions in protein evolution, stability, and enzymatic catalysis: insights from diverse analyses. PMID:24146608
Prediction and experimental validation of enzyme substrate specificity in protein structures. PMID:24145433
The strawberry pathogenesis-related 10 (PR-10) Fra a proteins control flavonoid biosynthesis by binding to metabolic intermediates. PMID:24133217
Structural insights into a novel interkingdom signaling circuit by cartography of the ligand-binding sites of the homologous quorum sensing LuxR-family. PMID:24132148
FFAS-3D: improving fold recognition by including optimized structural features and template re-ranking. PMID:24130308
'Naked' and hydrated conformers of the conserved core pentasaccharide of N-linked glycoproteins and its building blocks. PMID:24127839
Structure and function of a novel LD-carboxypeptidase a involved in peptidoglycan recycling. PMID:24123814
Extending RosettaDock with water, sugar, and pH for prediction of complex structures and affinities for CAPRI rounds 20-27. PMID:24123494
Definition and classification of evaluation units for CASP10. PMID:24123179
Insight into the molecular mechanism about lowered dihydrofolate binding affinity to dihydrofolate reductase-like 1 (DHFRL1). PMID:24122410
[Medicine from the computer]. PMID:24122221
Structural analysis of intermolecular interactions in the kinesin adaptor complex fasciculation and elongation protein zeta 1/ short coiled-coil protein (FEZ1/SCOCO). PMID:24116125
Probing the interaction of a therapeutic flavonoid, pinostrobin with human serum albumin: multiple spectroscopic and molecular modeling investigations. PMID:24116089
The structural basis of antibody-antigen recognition. PMID:24115948
Antibacterial mechanisms identified through structural systems pharmacology. PMID:24112686
Lipid exposure prediction enhances the inference of rotational angles of transmembrane helices. PMID:24112406
Esculetin suppresses proliferation of human colon cancer cells by directly targeting β-catenin. PMID:24104353
Molecular docking simulation studies on potent butyrylcholinesterase inhibitors obtained from microbial transformation of dihydrotestosterone. PMID:24103815
Advances in the REDCAT software package. PMID:24098943
Comparative molecular docking analysis of cytoplasmic dynein light chain DYNLL1 with pilin to explore the molecular mechanism of pathogenesis caused by Pseudomonas aeruginosa PAO. PMID:24098557
Ligand pose and orientational sampling in molecular docking. PMID:24098414
Personalized prediction of EGFR mutation-induced drug resistance in lung cancer. PMID:24092472
Molecular details of ligand selectivity determinants in a promiscuous β-glucan periplasmic binding protein. PMID:24090243
Funneling and frustration in the energy landscapes of some designed and simplified proteins. PMID:24089720
Autoreactivity and exceptional CDR plasticity (but not unusual polyspecificity) hinder elicitation of the anti-HIV antibody 4E10. PMID:24086134
Frequency response of a protein to local conformational perturbations. PMID:24086121
Frequency response of a protein to local conformational perturbations. PMID:24086121
Exploring the possible role of lysine acetylation on Entamoeba histolytica virulence: a focus on the dynamics of the actin cytoskeleton. PMID:24078923
Improved crystallographic structures using extensive combinatorial refinement. PMID:24076406
Investigating the selectivity of metalloenzyme inhibitors. PMID:24074025
Molecular dynamic simulation and inhibitor prediction of cysteine synthase structured model as a potential drug target for trichomoniasis. PMID:24073401
Structural Analysis of Cubane-Type Iron Clusters. PMID:24072952
A knowledge-based halogen bonding scoring function for predicting protein-ligand interactions. PMID:24072554
Combining solvent thermodynamic profiles with functionality maps of the Hsp90 binding site to predict the displacement of water molecules. PMID:24070451
A fusion-inhibiting peptide against Rift Valley fever virus inhibits multiple, diverse viruses. PMID:24069485
Cross-link guided molecular modeling with ROSETTA. PMID:24069194
Using the COREX/BEST server to model the native-state ensemble. PMID:24061926
Structural basis and targeting of the interaction between fibroblast growth factor-inducible 14 and tumor necrosis factor-like weak inducer of apoptosis. PMID:24056367
Prohibitin Interacts with envelope proteins of white spot syndrome virus and prevents infection in the red swamp crayfish, Procambarus clarkii. PMID:24049173
Solution NMR structure of CD1104B from pathogenic Clostridium difficile reveals a distinct α-helical architecture and provides first structural representative of protein domain family PF14203. PMID:24048810
Conformational flexibility of the leucine binding protein examined by protein domain coarse-grained molecular dynamics. PMID:24048570
Membrane protein orientation and refinement using a knowledge-based statistical potential. PMID:24047460
A novel clade of unique eukaryotic ribonucleotide reductase R2 subunits is exclusive to apicomplexan parasites. PMID:24046025
A molecular model of the full-length human NOD-like receptor family CARD domain containing 5 (NLRC5) protein. PMID:24044430
Comparative sequence and structure analysis reveals the conservation and diversity of nucleotide positions and their associated tertiary interactions in the riboswitches. PMID:24040136
In silico mechanistic profiling to probe small molecule binding to sulfotransferases. PMID:24039991
RosettaEPR: rotamer library for spin label structure and dynamics. PMID:24039810
Identification of PPARγ ligands with One-dimensional Drug Profile Matching. PMID:24039401
Homology modeling and ligand docking of Mitogen-activated protein kinase-activated protein kinase 5 (MK5). PMID:24034446
Protein crystallography for aspiring crystallographers or how to avoid pitfalls and traps in macromolecular structure determination. PMID:24034303
Mutational analysis of the stability of Psb27 from Synechocystis sp. PCC 6803: implications for models of Psb27 structure and binding to CP43. PMID:24030639
Analysis of protein thermostability enhancing factors in industrially important thermus bacteria species. PMID:24023508
Accounting for epistatic interactions improves the functional analysis of protein structures. PMID:24021383
Systematic analysis and prediction of pupylation sites in prokaryotic proteins. PMID:24019945
Predicting binding within disordered protein regions to structurally characterised peptide-binding domains. PMID:24019881
A comparative assessment and analysis of 20 representative sequence alignment methods for protein structure prediction. PMID:24018415
How community has shaped the Protein Data Bank. PMID:24010707
Effective harmonic potentials: insights into the internal cooperativity and sequence-specificity of protein dynamics. PMID:24009495
Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era. PMID:24009338
Proton fingerprints portray molecular structures: enhanced description of the 1H NMR spectra of small molecules. PMID:24007197
Automated identification of RNA 3D modules with discriminative power in RNA structural alignments. PMID:24005040
Molecular models and mutational analyses of plant specifier proteins suggest active site residues and reaction mechanism. PMID:23999604
Influence of Grid Spacing in Poisson-Boltzmann Equation Binding Energy Estimation. PMID:23997692
Influence of C-H...O interactions on the structural stability of β-lactamases. PMID:23996409
Protein depth calculation and the use for improving accuracy of protein fold recognition. PMID:23992298
Structural phylogenomics retrodicts the origin of the genetic code and uncovers the evolutionary impact of protein flexibility. PMID:23991065
Comparative analyses of lipoprotein lipase, hepatic lipase, and endothelial lipase, and their binding properties with known inhibitors. PMID:23991054
On the importance of polar interactions for complexes containing intrinsically disordered proteins. PMID:23990768
Design and exploratory data analysis of a second generation of dendrimer prodrugs potentially antichagasic and leishmanicide. PMID:23990201
A plausible mechanism for the antimalarial activity of artemisinin: A computational approach. PMID:23985481
MONA - Interactive manipulation of molecule collections. PMID:23985157
Navigating traditional chinese medicine network pharmacology and computational tools. PMID:23983798
Deciphering the glycan preference of bacterial lectins by glycan array and molecular docking with validation by microcalorimetry and crystallography. PMID:23976992
Computational Analysis of N-acetyl transferase in Tribolium castaneum. PMID:23976826
Elucidating the evolutionary conserved DNA-binding specificities of WRKY transcription factors by molecular dynamics and in vitro binding assays. PMID:23975197
Protein structure validation and identification from unassigned residual dipolar coupling data using 2D-PDPA. PMID:23973992
Characterizing a histidine switch controlling pH-dependent conformational changes of the influenza virus hemagglutinin. PMID:23972851
Bioinformatics resources and tools for conformational B-cell epitope prediction. PMID:23970944
Solution NMR structures provide first structural coverage of the large protein domain family PF08369 and complementary structural coverage of dark operative protochlorophyllide oxidoreductase complexes. PMID:23963952
HippDB: a database of readily targeted helical protein-protein interactions. PMID:23958730
Uses of phage display in agriculture: sequence analysis and comparative modeling of late embryogenesis abundant client proteins suggest protein-nucleic acid binding functionality. PMID:23956788
Binding polymorphism in the DNA bound state of the Pdx1 homeodomain. PMID:23950697
Highly potent HIV-1 protease inhibitors with novel tricyclic P2 ligands: design, synthesis, and protein-ligand X-ray studies. PMID:23947685
Organism-adapted specificity of the allosteric regulation of pyruvate kinase in lactic acid bacteria. PMID:23946717
Assessment of protein disorder region predictions in CASP10. PMID:23946100
A creature with a hundred waggly tails: intrinsically disordered proteins in the ribosome. PMID:23942625
Menthol binding and inhibition of α7-nicotinic acetylcholine receptors. PMID:23935840
Impaired oxidoreduction by 11β-hydroxysteroid dehydrogenase 1 results in the accumulation of 7-oxolithocholic acid. PMID:23933573
A computational exploration of the interactions of the green tea polyphenol (-)-Epigallocatechin 3-Gallate with cardiac muscle troponin C. PMID:23923004
Molecular basis of HHQ biosynthesis: molecular dynamics simulations, enzyme kinetic and surface plasmon resonance studies. PMID:23916145
Evolution of the key alkaloid enzyme putrescine N-methyltransferase from spermidine synthase. PMID:23908659
Computational design of a full-length model of HIV-1 integrase: modeling of new inhibitors and comparison of their calculated binding energies with those previously studied. PMID:23907552
Distributions of amino acids suggest that certain residue types more effectively determine protein secondary structure. PMID:23907551
β-Bulges: extensive structural analyses of β-sheets irregularities. PMID:23904395
[Medicine from the computer]. PMID:23903763
eVolver: an optimization engine for evolving protein sequences to stabilize the respective structures. PMID:23902875
Solving the molecular distance geometry problem with inaccurate distance data. PMID:23901894
NetMHCIIpan-3.0, a common pan-specific MHC class II prediction method including all three human MHC class II isotypes, HLA-DR, HLA-DP and HLA-DQ. PMID:23900783
The good, the bad and the dubious: VHELIBS, a validation helper for ligands and binding sites. PMID:23895374
Structure of allergens and structure based epitope predictions. PMID:23891546
Nanomechanics of collagen microfibrils. PMID:23885342
Adjudin disrupts spermatogenesis by targeting drug transporters: Lesson from the breast cancer resistance protein (BCRP). PMID:23885306
Finding non-crystallographic symmetry in density maps of macromolecular structures. PMID:23881095
An overview of tools for the validation of protein NMR structures. PMID:23877928
Re-docking scheme for generating near-native protein complexes by assembling residue interaction fingerprints. PMID:23874954
Structural and functional characterisation of TesA - a novel lysophospholipase A from Pseudomonas aeruginosa. PMID:23874889
Structural analysis of mitochondrial mutations reveals a role for bigenomic protein interactions in human disease. PMID:23874847
Identification of a novel sulfonamide non-nucleoside reverse transcriptase inhibitor by a phenotypic HIV-1 full replication assay. PMID:23874756
Effects of NMR spectral resolution on protein structure calculation. PMID:23874675
Unique mechanism of the interaction between honey bee toxin TPNQ and rKir1.1 potassium channel explored by computational simulations: insights into the relative insensitivity of channel towards animal toxins. PMID:23874410
Target essentiality and centrality characterize drug side effects. PMID:23874169
Mesoscale modeling of multi-protein-DNA assemblies: the role of the catabolic activator protein in Lac-repressor-mediated looping. PMID:23874000
DockRank: ranking docked conformations using partner-specific sequence homology-based protein interface prediction. PMID:23873600
β-Keto esters from ketones and ethyl chloroformate: a rapid, general, efficient synthesis of pyrazolones and their antimicrobial, in silico and in vitro cytotoxicity studies. PMID:23870758
Adding diverse noncanonical backbones to rosetta: enabling peptidomimetic design. PMID:23869206
CREDO: a structural interactomics database for drug discovery. PMID:23868908
Evidence of direct complementary interactions between messenger RNAs and their cognate proteins. PMID:23868089
Structure prediction of partial-length protein sequences. PMID:23867606
in Silico analysis of Escherichia coli polyphosphate kinase (PPK) as a novel antimicrobial drug target and its high throughput virtual screening against PubChem library. PMID:23861568
An innate twist between Crick's wobble and Watson-Crick base pairs. PMID:23861536
Interaction between extracellular lipase LipA and the polysaccharide alginate of Pseudomonas aeruginosa. PMID:23848942
MORPH-PRO: a novel algorithm and web server for protein morphing. PMID:23844614
Residue-level prediction of HIV-1 antibody epitopes based on neutralization of diverse viral strains. PMID:23843642
Identification of methyllysine peptides binding to chromobox protein homolog 6 chromodomain in the human proteome. PMID:23842000
Fungal effector Ecp6 outcompetes host immune receptor for chitin binding through intrachain LysM dimerization. PMID:23840930
Novel hybrid virtual screening protocol based on molecular docking and structure-based pharmacophore for discovery of methionyl-tRNA synthetase inhibitors as antibacterial agents. PMID:23839093
PFClust: a novel parameter free clustering algorithm. PMID:23819480
Evaluating template-based and template-free protein-protein complex structure prediction. PMID:23818491
Weak operator binding enhances simulated Lac repressor-mediated DNA looping. PMID:23818216
[Medicine from the computer]. PMID:23817844
Prediction of Long Loops with Embedded Secondary Structure using the Protein Local Optimization Program. PMID:23814507
Effect of the abortive infection mechanism and type III toxin/antitoxin system AbiQ on the lytic cycle of Lactococcus lactis phages. PMID:23813728
DockoMatic 2.0: high throughput inverse virtual screening and homology modeling. PMID:23808933
Protein pocket and ligand shape comparison and its application in virtual screening. PMID:23807262
Drug Promiscuity in PDB: Protein Binding Site Similarity Is Key. PMID:23805191
Formation of threohydrobupropion from bupropion is dependent on 11β-hydroxysteroid dehydrogenase 1. PMID:23804523
Integrative relational machine-learning for understanding drug side-effect profiles. PMID:23802887
Unleashing the power of meta-threading for evolution/structure-based function inference of proteins. PMID:23802014
MuPIT interactive: webserver for mapping variant positions to annotated, interactive 3D structures. PMID:23793516
AutoGrow 3.0: an improved algorithm for chemically tractable, semi-automated protein inhibitor design. PMID:23792207
Dissecting disease inheritance modes in a three-dimensional protein network challenges the "guilt-by-association" principle. PMID:23791107
Nanoindentation of 35 virus capsids in a molecular model: relating mechanical properties to structure. PMID:23785395
Modulating the intrinsic disorder in the cytoplasmic domain alters the biological activity of the N-methyl-D-aspartate-sensitive glutamate receptor. PMID:23782697
A structural basis for IκB kinase 2 activation via oligomerization-dependent trans auto-phosphorylation. PMID:23776406
Sampling and scoring: a marriage made in heaven. PMID:23775627
Tracking the interplay between bound peptide and the lid domain of DnaK, using molecular dynamics. PMID:23774839
In silico prediction of a disease-associated STIL mutant and its affect on the recruitment of centromere protein J (CENPJ). PMID:23772360
Isolation and characterization of mutant Sinorhizobium meliloti NodD1 proteins with altered responses to luteolin. PMID:23772067
Computational analysis of protein-protein interfaces involving an alpha helix: insights for terphenyl-like molecules binding. PMID:23768251
bioNerDS: exploring bioinformatics' database and software use through literature mining. PMID:23768135
TIPdb: a database of anticancer, antiplatelet, and antituberculosis phytochemicals from indigenous plants in Taiwan. PMID:23766708
TIMBAL v2: update of a database holding small molecules modulating protein-protein interactions. PMID:23766369
Cloud computing for protein-ligand binding site comparison. PMID:23762824
A Saccharomyces cerevisiae assay system to investigate ligand/AdipoR1 interactions that lead to cellular signaling. PMID:23762377
Early relaxation dynamics in the LC 13 T cell receptor in reaction to 172 altered peptide ligands: a molecular dynamics simulation study. PMID:23762240
The Aquaporin Channel Repertoire of the Tardigrade Milnesium tardigradum. PMID:23761966
VLDP web server: a powerful geometric tool for analysing protein structures in their environment. PMID:23761450
Utilizing protein structure to identify non-random somatic mutations. PMID:23758891
ΔΔPT: a comprehensive toolbox for the analysis of protein motion. PMID:23758746
Alternative splicing tends to avoid partial removals of protein-protein interaction sites. PMID:23758645
Free energy profiles of base flipping in intercalative polycyclic aromatic hydrocarbon-damaged DNA duplexes: energetic and structural relationships to nucleotide excision repair susceptibility. PMID:23758590
Scrutinizing MHC-I binding peptides and their limits of variation. PMID:23754940
Structure and function of the T-loop structural motif in noncoding RNAs. PMID:23754657
Under-folded proteins: Conformational ensembles and their roles in protein folding, function, and pathogenesis. PMID:23754493
Aromatic-aromatic interactions: analysis of π-π interactions in interleukins and TNF proteins. PMID:23750094
DNA phosphate crowding correlates with protein cationic side chain density and helical curvature in protein/DNA crystal structures. PMID:23748560
Characterizing protein domain associations by Small-molecule ligand binding. PMID:23745168
Structural systems biology evaluation of metabolic thermotolerance in Escherichia coli. PMID:23744946
The role of tyrosine sulfation in the dimerization of the CXCR4:SDF-1 complex. PMID:23740770
Rice mitogen activated protein kinase kinase and mitogen activated protein kinase interaction network revealed by in-silico docking and yeast two-hybrid approaches. PMID:23738013
SPACER: Server for predicting allosteric communication and effects of regulation. PMID:23737445
Functional diversity and structural disorder in the human ubiquitination pathway. PMID:23734257
Computer-Aided Approaches for Targeting HIVgp41. PMID:23730525
Biophysical screening for the discovery of small-molecule ligands. PMID:23729259
PPIcons: identification of protein-protein interaction sites in selected organisms. PMID:23729008
Tumor necrosis factor receptor superfamily 10B (TNFRSF10B): an insight from structure modeling to virtual screening for designing drug against head and neck cancer. PMID:23724937
Adaptive selection on bracovirus genomes drives the specialization of Cotesia parasitoid wasps. PMID:23724046
BeAtMuSiC: Prediction of changes in protein-protein binding affinity on mutations. PMID:23723246
SAHBNET, an accessible surface-based elastic network: an application to membrane protein. PMID:23722660
Ab Initio structure prediction for Escherichia coli: towards genome-wide protein structure modeling and fold assignment. PMID:23719418
IMAAAGINE: a webserver for searching hypothetical 3D amino acid side chain arrangements in the Protein Data Bank. PMID:23716645
R3D Align web server for global nucleotide to nucleotide alignments of RNA 3D structures. PMID:23716643
Structure and mechanism of maximum stability of isolated alpha-helical protein domains at a critical length scale. PMID:23708839
Combined sequence-based and genetic mapping analysis of complex traits in outbred rats. PMID:23708188
Small molecule agonist of very late antigen-4 (VLA-4) integrin induces progenitor cell adhesion. PMID:23703610
Vienna-PTM web server: a toolkit for MD simulations of protein post-translational modifications. PMID:23703210
Differential geometric analysis of alterations in MH α-helices. PMID:23703160
QA-RecombineIt: a server for quality assessment and recombination of protein models. PMID:23700309
Ligand binding site similarity identification based on chemical and geometric similarity. PMID:23700221
Comprehensive database of Chorismate synthase enzyme from shikimate pathway in pathogenic bacteria. PMID:23697663
ExtremeDB: a unified web repository of extremophilic archaea and bacteria. PMID:23696792
Cross-species protein interactome mapping reveals species-specific wiring of stress response pathways. PMID:23695164
The Missing Heritability in T1D and Potential New Targets for Prevention. PMID:23691517
Comprehensive genome-wide survey, genomic constitution and expression profiling of the NAC transcription factor family in foxtail millet (Setaria italica L.). PMID:23691254
Identifying sequence determinants of reduction potentials of metalloproteins. PMID:23690205
NAFlex: a web server for the study of nucleic acid flexibility. PMID:23685436
Structure-based non-canonical amino acid design to covalently crosslink an antibody-antigen complex. PMID:23680795
Catalytic site identification--a web server to identify catalytic site structural matches throughout PDB. PMID:23680785
CovalentDock Cloud: a web server for automated covalent docking. PMID:23677616
Endocytosis of synaptic ADAM10 in neuronal plasticity and Alzheimer's disease. PMID:23676497
Insight into the 3D structure of ADP-glucose pyrophosphorylase from rice (Oryza sativa L.). PMID:23674369
Identification of antagonists to the vasotocin receptor sub-type 4 (VT4R) involved in stress by molecular modelling and verification using anterior pituitary cells. PMID:23672311
Computational identification and analysis of arsenate reductase protein in Cronobacter sakazakii ATCC BAA-894 suggests potential microorganism for reducing arsenate. PMID:23666632
Cloning, in silico characterization and induction of TiKpp2 MAP kinase in Tilletia indica under the influence of host factor(s) from wheat spikes. PMID:23666057
Molecular dynamics simulation of tryptophan hydroxylase-1: binding modes and free energy analysis to phenylalanine derivative inhibitors. PMID:23665899
Modular aspects of kinesin force generation machinery. PMID:23663840
Structural characterization of human histidine triad nucleotide-binding protein 2, a member of the histidine triad superfamily. PMID:23659632
Tryptogalinin is a tick Kunitz serine protease inhibitor with a unique intrinsic disorder. PMID:23658744
Stability mechanisms of a thermophilic laccase probed by molecular dynamics. PMID:23658618
Molecular and structural insight into lysine selection on substrate and ubiquitin lysine 48 by the ubiquitin-conjugating enzyme Cdc34. PMID:23656784
Three-Dimensional Visualizations in Teaching Genomics and Bioinformatics: Mutations in HIV Envelope Proteins and Their Consequences for Vaccine Design. PMID:23653552
Targeted editing of goat genome with modular-assembly zinc finger nucleases based on activity prediction by computational molecular modeling. PMID:23645027
Analyzing and building nucleic acid structures with 3DNA. PMID:23644419
Molecular mechanism of misfolding and aggregation of Aβ(13-23). PMID:23642026
DNA marker applications to molecular genetics and genomics in tomato. PMID:23641178
Memoir: template-based structure prediction for membrane proteins. PMID:23640332
Virtual screening for oseltamivir-resistant a (H5N1) influenza neuraminidase from traditional Chinese medicine database: a combined molecular docking with molecular dynamics approach. PMID:23638404
Malleable ribonucleoprotein machine: protein intrinsic disorder in the Saccharomyces cerevisiae spliceosome. PMID:23638354
A study of the mechanism of the chaperone-like function of an scFv of human creatine kinase by computer simulation. PMID:23637984
Understanding thermostability factors of Aspergillus niger PhyA phytase: a molecular dynamics study. PMID:23636517
Design of Thymidine Analogues Targeting Thymidilate Kinase of Mycobacterium tuberculosis. PMID:23634301
New Perspectives on How to Discover Drugs from Herbal Medicines: CAM's Outstanding Contribution to Modern Therapeutics. PMID:23634172
A transcriptome-proteome integrated network identifies endoplasmic reticulum thiol oxidoreductase (ERp57) as a hub that mediates bone metastasis. PMID:23625662
Synthesis and biological evaluation of cationic fullerene quinazolinone conjugates and their binding mode with modeled Mycobacterium tuberculosis hypoxanthine-guanine phosphoribosyltransferase enzyme. PMID:23625031
Accurate assessment of mass, models and resolution by small-angle scattering. PMID:23619693
Conformational readout of RNA by small ligands. PMID:23618839
Structural and functional studies of S-adenosyl-L-methionine binding proteins: a ligand-centric approach. PMID:23617634
CSAR data set release 2012: ligands, affinities, complexes, and docking decoys. PMID:23617227
Increased polyamines alter chromatin and stabilize autoantigens in autoimmune diseases. PMID:23616785
Two crystal structures of Bombyx mori lipoprotein 3 - structural characterization of a new 30-kDa lipoprotein family member. PMID:23613829
Functional and structural analysis of C-terminal BRCA1 missense variants. PMID:23613828
Identification and characterization of a previously undescribed family of sequence-specific DNA-binding domains. PMID:23610392
LISE: a server using ligand-interacting and site-enriched protein triangles for prediction of ligand-binding sites. PMID:23609546
PRR repeats in the intracellular domain of KISS1R are important for its export to cell membrane. PMID:23608644
Inhibitors for the hepatitis C virus RNA polymerase explored by SAR with advanced machine learning methods. PMID:23608107
Identifying residues that cause pH-dependent reduction potentials. PMID:23607577
Stereo-selective binding of monoclonal antibodies to the poly-γ-D-glutamic acid capsular antigen of Bacillus anthracis. PMID:23602451
INstruct: a database of high-quality 3D structurally resolved protein interactome networks. PMID:23599502
A comparative study of interaction of tetracycline with several proteins using time resolved anisotropy, phosphorescence, docking and FRET. PMID:23593355
DomHR: accurately identifying domain boundaries in proteins using a hinge region strategy. PMID:23593247
Exploiting conformational ensembles in modeling protein-protein interactions on the proteome scale. PMID:23590674
Protein complexes are under evolutionary selection to assemble via ordered pathways. PMID:23582331
Sequence and conformation effects on ionization potential and charge distribution of homo-nucleobase stacks using M06-2X hybrid density functional theory calculations. PMID:23582046
Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments. PMID:23579614
A general and robust ray-casting-based algorithm for triangulating surfaces at the nanoscale. PMID:23577073
Recurrent structural motifs in non-homologous protein structures. PMID:23574940
Plant High-Affinity Potassium (HKT) Transporters involved in salinity tolerance: structural insights to probe differences in ion selectivity. PMID:23571493
Clustering evolving proteins into homologous families. PMID:23566217
Structure based descriptors for the estimation of colloidal interactions and protein aggregation propensities. PMID:23565169
MH2c: Characterization of major histocompatibility α-helices - an information criterion approach. PMID:23564964
Retrospective molecular docking study of WY-25105 ligand to β-secretase and bias of the three-dimensional structure flexibility. PMID:23564327
Mammalian neuronal sodium channel blocker μ-conotoxin BuIIIB has a structured N-terminus that influences potency. PMID:23557677
Understanding the specificity of human Galectin-8C domain interactions with its glycan ligands based on molecular dynamics simulations. PMID:23555773
Rampant exchange of the structure and function of extramembrane domains between membrane and water soluble proteins. PMID:23555228
Analysis of physicochemical and structural properties determining HIV-1 coreceptor usage. PMID:23555214
Amino Acid derivatives as new zinc binding groups for the design of selective matrix metalloproteinase inhibitors. PMID:23555050
Computational interaction analysis of organophosphorus pesticides with different metabolic proteins in humans. PMID:23554709
Comprehensive prediction in 78 human cell lines reveals rigidity and compactness of transcription factor dimers. PMID:23554463
Structure-based network analysis of an evolved G protein-coupled receptor homodimer interface. PMID:23553730
Homology modeling and virtual screening approaches to identify potent inhibitors of VEB-1 β-lactamase. PMID:23547944
Structure of glutaminyl cyclase from Drosophila melanogaster in space group I4. PMID:23545638
Organophosphorus acid anhydrolase from Alteromonas macleodii: structural study and functional relationship to prolidases. PMID:23545636
Detection and characterization of megasatellites in orthologous and nonorthologous genes of 21 fungal genomes. PMID:23543670
Conformational heterogeneity within the LID domain mediates substrate binding to Escherichia coli adenylate kinase: function follows fluctuations. PMID:23543318
Non-canonical H-bonds in β-lactamases: importance of C-H···π interactions. PMID:23543235
Specificity of Processing α-glucosidase I is guided by the substrate conformation: crystallographic and in silico studies. PMID:23536181
On the relevance of sophisticated structural annotations for disulfide connectivity pattern prediction. PMID:23533562
Immunosuppression by co-stimulatory molecules: inhibition of CD2-CD48/CD58 interaction by peptides from CD2 to suppress progression of collagen-induced arthritis in mice. PMID:23530775
A benchmark server using high resolution protein structure data, and benchmark results for membrane helix predictions. PMID:23530628
Docking challenge: protein sampling and molecular docking performance. PMID:23530568
Description of local and global shape properties of protein helices. PMID:23529181
Protein dynamics and motions in relation to their functions: several case studies and the underlying mechanisms. PMID:23527883
Insight the C-site pocket conformational changes responsible for sirtuin 2 activity using molecular dynamics simulations. PMID:23527151
Structural insights into putative molybdenum cofactor biosynthesis protein C (MoaC2) from Mycobacterium tuberculosis H37Rv. PMID:23526978
Formation of cystine slipknots in dimeric proteins. PMID:23520470
Local network patterns in protein-protein interfaces. PMID:23520460
Protein molecular surface mapped at different geometrical resolutions. PMID:23516572
Kinetic and structural evidences on human prolidase pathological mutants suggest strategies for enzyme functional rescue. PMID:23516557
A unified conformational selection and induced fit approach to protein-peptide docking. PMID:23516555
Restricted N-glycan conformational space in the PDB and its implication in glycan structure modeling. PMID:23516343
Function prediction from networks of local evolutionary similarity in protein structure. PMID:23514548
Protein-ligand binding region prediction (PLB-SAVE) based on geometric features and CUDA acceleration. PMID:23514235
Concomitant prediction of function and fold at the domain level with GO-based profiles. PMID:23514233
Prediction of conformational epitopes with the use of a knowledge-based energy function and geometrically related neighboring residue characteristics. PMID:23514199
A single intact ATPase site of the ABC transporter BtuCD drives 5% transport activity yet supports full in vivo vitamin B12 utilization. PMID:23513227
Quantitative residue-level structure-evolution relationships in the yeast membrane proteome. PMID:23512408
Predicting β-turns in protein using kernel logistic regression. PMID:23509793
The human gene connectome as a map of short cuts for morbid allele discovery. PMID:23509278
Multiphasic analysis of whole exome sequencing data identifies a novel mutation of ACTG1 in a nonsyndromic hearing loss family. PMID:23506231
Predicting where small molecules bind at protein-protein interfaces. PMID:23505538
Combined computational design of a zinc-binding site and a protein-protein interaction: one open zinc coordination site was not a robust hotspot for de novo ubiquitin binding. PMID:23504819
myo-inositol and D-ribose ligand discrimination in an ABC periplasmic binding protein. PMID:23504019
Discrete molecular dynamics study of oligomer formation by N-terminally truncated amyloid β-protein. PMID:23500806
NightShift: NMR shift inference by general hybrid model training--a framework for NMR chemical shift prediction. PMID:23496927
Identification of novel Interleukin-2 inhibitors through computational approaches. PMID:23494734
Computational analysis of C-reactive protein for assessment of molecular dynamics and interaction properties. PMID:23494263
A Bioinformatics Approach for Homology Modeling and Binding Site Identification of Triosephosphate Isomerase from Plasmodium falciparum 3D7. PMID:23492818
On the structural context and identification of enzyme catalytic residues. PMID:23484160
Game on, science - how video game technology may help biologists tackle visualization challenges. PMID:23483961
Protein-protein docking with F(2)Dock 2.0 and GB-rerank. PMID:23483883
Structural Variations of Human Glucokinase Glu256Lys in MODY2 Condition Using Molecular Dynamics Study. PMID:23476789
Thermal aggregation of recombinant protective antigen: aggregate morphology and growth rate. PMID:23476645
Hydrogen bond strengths in phosphorylated and sulfated amino acid residues. PMID:23472106
Behavior of solvent-exposed hydrophobic groove in the anti-apoptotic Bcl-XL protein: clues for its ability to bind diverse BH3 ligands from MD simulations. PMID:23468841
A dynamic model of the proteins that form the initial iron-sulfur cluster biogenesis machinery in yeast mitochondria. PMID:23463383
Allosteric regulation of serine protease HtrA2 through novel non-canonical substrate binding pocket. PMID:23457469
Systems modelling of NHEJ reveals the importance of redox regulation of Ku70/80 in the dynamics of dna damage foci. PMID:23457464
A mass weighted chemical elastic network model elucidates closed form domain motions in proteins. PMID:23456820
Recent advances in computational methods for nuclear magnetic resonance data processing. PMID:23453016
Direct targeting of MEK1/2 and RSK2 by silybin induces cell-cycle arrest and inhibits melanoma cell growth. PMID:23447564
Discovery of novel focal adhesion kinase inhibitors using a hybrid protocol of virtual screening approach based on multicomplex-based pharmacophore and molecular docking. PMID:23443087
Computational assembly of polymorphic amyloid fibrils reveals stable aggregates. PMID:23442919
Protein Structure Idealization: How accurately is it possible to model protein structures with dihedral angles? PMID:23442792
Free energy landscape for the binding process of Huperzine A to acetylcholinesterase. PMID:23440190
CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction. PMID:23435231
Detection of protein catalytic sites in the biomedical literature. PMID:23424147
MetaSeq: privacy preserving meta-analysis of sequencing-based association studies. PMID:23424140
Insight towards the conserved water mediated recognition of catalytic and structural Zn(+2) ions in human Matrix Metalloproteinase-8 enzyme: A study by MD-simulation methods. PMID:23423544
Prediction of temperature factors from protein sequence. PMID:23422595
Proteome-wide prediction of self-interacting proteins based on multiple properties. PMID:23422585
Local conformational changes in the DNA interfaces of proteins. PMID:23418514
Prediction of contact matrix for protein-protein interaction. PMID:23418186
Breaking the aggregation of the monoclonal antibody bevacizumab (avastin®) by dexamethasone phosphate: insights from molecular modelling and asymmetrical flow field-flow fractionation. PMID:23412914
Discovery of novel Trypanosoma brucei phosphodiesterase B1 inhibitors by virtual screening against the unliganded TbrPDEB1 crystal structure. PMID:23409953
In silico Evaluation of Crosslinking Effects on Denaturant m(eq) values and ΔCp upon Protein Unfolding. PMID:23408172
Interactome3D: adding structural details to protein networks. PMID:23399932
Interactome3D: adding structural details to protein networks. PMID:23399932
Role of P-glycoprotein at the blood-testis barrier on adjudin distribution in the testis: a revisit of recent data. PMID:23397632
Experience with exchange and archiving of raw data: comparison of data from two diffractometers and four software packages on a series of lysozyme crystals. PMID:23396873
Searching for an endogenous anti-Alzheimer molecule: identifying small molecules in the brain that slow Alzheimer disease progression by inhibition of ß-amyloid aggregation. PMID:23394811
Prediction of vitamin interacting residues in a vitamin binding protein using evolutionary information. PMID:23387468
Visualizing ligand molecules in Twilight electron density. PMID:23385767
Rigid Body Energy Minimization on Manifolds for Molecular Docking. PMID:23382659
Bioengineering of AAV2 capsid at specific serine, threonine, or lysine residues improves its transduction efficiency in vitro and in vivo. PMID:23379478
Visualization of protein interaction networks: problems and solutions. PMID:23368786
Structure-based in silico identification of ubiquitin-binding domains provides insights into the ALIX-V:ubiquitin complex and retrovirus budding. PMID:23361315
Seq2Ref: a web server to facilitate functional interpretation. PMID:23356573
Enterotoxigenic Escherichia coli CS1 pilus: not one structure but several. PMID:23354749
Temperature and urea have opposing impacts on polyproline II conformational bias. PMID:23350874
Protein surface dynamics: interaction with water and small solutes. PMID:23345909
Toward correct protein folding potentials. PMID:23345867
Theoretical Characterization of the Long-range Attraction between G-actin Molecules through the Excluded Volume Effect. PMID:23345780
A molecular-modeling toolbox aimed at bridging the gap between medicinal chemistry and computational sciences. PMID:23344039
Evolutionary conservation of the polyproline II conformation surrounding intrinsically disordered phosphorylation sites. PMID:23341186
Computational design of glutamate dehydrogenase in Bacillus subtilis natto. PMID:23338837
Trendspotting in the Protein Data Bank. PMID:23337870
Predicting PDZ domain mediated protein interactions from structure. PMID:23336252
High-resolution analysis and functional mapping of cleavage sites and substrate proteins of furin in the human proteome. PMID:23335997
APoc: large-scale identification of similar protein pockets. PMID:23335017
Improving protocols for protein mapping through proper comparison to crystallography data. PMID:23327200
A consensus method for the prediction of 'aggregation-prone' peptides in globular proteins. PMID:23326595
Structure prediction and validation of the ERK8 kinase domain. PMID:23326322
Ligand-based Pharmacophore Modeling; Atom-based 3D-QSAR Analysis and Molecular Docking Studies of Phosphoinositide-Dependent Kinase-1 Inhibitors. PMID:23325995
Breaking in: human metapneumovirus fusion and entry. PMID:23325326
Modeling of Anopheles minimus Mosquito NADPH-cytochrome P450 oxidoreductase (CYPOR) and mutagenesis analysis. PMID:23325047
Recognition of methylated peptides by Drosophila melanogaster polycomb chromodomain. PMID:23320494
A structural-based strategy for recognition of transcription factor binding sites. PMID:23320072
Bacterial feeding, Leishmania infection and distinct infection routes induce differential defensin expression in Lutzomyia longipalpis. PMID:23311993
A genetic polymorphism evolving in parallel in two cell compartments and in two clades. PMID:23311980
On the molecular basis of D-bifunctional protein deficiency type III. PMID:23308274
A unified model of the GABA(A) receptor comprising agonist and benzodiazepine binding sites. PMID:23308109
Biomacromolecular quantitative structure-activity relationship (BioQSAR): a proof-of-concept study on the modeling, prediction and interpretation of protein-protein binding affinity. PMID:23306464
Dynamic regulation of phenylalanine hydroxylase by simulated redox manipulation. PMID:23300845
Activity cliffs in PubChem confirmatory bioassays taking inactive compounds into account. PMID:23296990
Fluorescence resonance energy transfer glucose sensor from site-specific dual labeling of glucose/galactose binding protein using ligand protection. PMID:23294773
Finite Element Estimation of Protein-Ligand Association Rates with Post-Encounter Effects: Applications to Calcium binding in Troponin C and SERCA. PMID:23293662
Discovery of a chemical probe for the L3MBTL3 methyllysine reader domain. PMID:23292653
PubChem3D: conformer ensemble accuracy. PMID:23289532
The nuclear magnetic resonance of CCCC RNA reveals a right-handed helix, and revised parameters for AMBER force field torsions improve structural predictions from molecular dynamics. PMID:23286901
The difficulty of protein structure alignment under the RMSD. PMID:23286762
Comparative analysis of homology models of the AH receptor ligand binding domain: verification of structure-function predictions by site-directed mutagenesis of a nonfunctional receptor. PMID:23286227
Sanjeevini: a freely accessible web-server for target directed lead molecule discovery. PMID:23282245
Large-scale reverse docking profiles and their applications. PMID:23282219
B-cell epitope prediction through a graph model. PMID:23281855
Preferential binding of fisetin to the native state of bovine serum albumin: spectroscopic and docking studies. PMID:23277393
Anti hyperglycaemic study of natural inhibitors for Insulin receptor. PMID:23275719
Identification of small molecule inhibitors against UBE2C by using docking studies. PMID:23275705
Placement of molecules in (not out of) the cell. PMID:23275157
Objective assessment of cancer genes for drug discovery. PMID:23274470
Polypharmacology: drug discovery for the future. PMID:23272792
Structural and functional analysis of multi-interface domains. PMID:23272073
NetMODE: network motif detection without Nauty. PMID:23272055
A consistent description of HYdrogen bond and DEhydration energies in protein-ligand complexes: methods behind the HYDE scoring function. PMID:23269578
The twilight zone of cis element alignments. PMID:23268451
Plucking the high hanging fruit: a systematic approach for targeting protein-protein interactions. PMID:23267671
Toward a three-dimensional view of protein networks between species. PMID:23267356
Understanding the general packing rearrangements required for successful template based modeling of protein structure from a CASP experiment. PMID:23266765
In vivo translation rates can substantially delay the cotranslational folding of the Escherichia coli cytosolic proteome. PMID:23256155
Identification of MDP (muramyl dipeptide)-binding key domains in NOD2 (nucleotide-binding and oligomerization domain-2) receptor of Labeo rohita. PMID:23255217
Modelling dynamics in protein crystal structures by ensemble refinement. PMID:23251785
T-cell receptors binding orientation over peptide/MHC class I is driven by long-range interactions. PMID:23251658
Binding modes of peptidomimetics designed to inhibit STAT3. PMID:23251591
Discrete kinetic models from funneled energy landscape simulations. PMID:23251375
Molecular characterization of farnesyl pyrophosphate synthase from Bacopa monniera by comparative modeling and docking studies. PMID:23251041
Free enthalpies of replacing water molecules in protein binding pockets. PMID:23247390
Conservation of the three-dimensional structure in non-homologous or unrelated proteins. PMID:23244440
Mutual information and variants for protein domain-domain contact prediction. PMID:23244412
Describing sequence-ensemble relationships for intrinsically disordered proteins. PMID:23240611
What can we learn from the evolution of protein-ligand interactions to aid the design of new therapeutics? PMID:23240060
Predicting permanent and transient protein-protein interfaces. PMID:23239312
Drug cocktail optimization in chemotherapy of cancer. PMID:23236419
Secondary structure, a missing component of sequence-based minimotif definitions. PMID:23236358
Utilization of protein intrinsic disorder knowledge in structural proteomics. PMID:23232152
Discovery, synthesis, and structure-based optimization of a series of N-(tert-butyl)-2-(N-arylamido)-2-(pyridin-3-yl) acetamides (ML188) as potent noncovalent small molecule inhibitors of the severe acute respiratory syndrome coronavirus (SARS-CoV) 3CL protease. PMID:23231439
Characterizing the effects of the protein environment on the reduction potentials of metalloproteins. PMID:23229112
Evolution of general transcription factors. PMID:23229069
Identification of PPARgamma partial agonists of natural origin (I): development of a virtual screening procedure and in vitro validation. PMID:23226391
Halogen bonding (X-bonding): a biological perspective. PMID:23225628
Computational insights into the selectivity mechanism of APP-IP over matrix metalloproteinases. PMID:23224743
Education catching up with science: preparing students for three-dimensional literacy in cell biology. PMID:23222839
Generation and characterization of monospecific and bispecific hexavalent trimerbodies. PMID:23221741
Contribution of V(H) replacement products to the generation of anti-HIV antibodies. PMID:23220404
CDR-H3 diversity is not required for antigen recognition by synthetic antibodies. PMID:23219464
Identification of nucleotide-binding sites in protein structures: a novel approach based on nucleotide modularity. PMID:23209685
Wiki-pi: a web-server of annotated human protein-protein interactions to aid in discovery of protein function. PMID:23209562
CHARMM-GUI Ligand Binder for absolute binding free energy calculations and its application. PMID:23205773
Protein Simulation Data in the Relational Model. PMID:23204646
2P2Idb: a structural database dedicated to orthosteric modulation of protein-protein interactions. PMID:23203891
A generic force field for protein coarse-grained molecular dynamics simulation. PMID:23203075
Influence of the O-phosphorylation of serine, threonine and tyrosine in proteins on the amidic ¹⁵N chemical shielding anisotropy tensors. PMID:23202985
Proteins of unknown function in the Protein Data Bank (PDB): an inventory of true uncharacterized proteins and computational tools for their analysis. PMID:23202924
Using the unfolded state as the reference state improves the performance of statistical potentials. PMID:23199923
New pockets in dengue virus 2 surface identified by molecular dynamics simulation. PMID:23197323
PTMcode: a database of known and predicted functional associations between post-translational modifications in proteins. PMID:23193284
The RCSB Protein Data Bank: new resources for research and education. PMID:23193259
A solvated ligand rotamer approach and its application in computational protein design. PMID:23192355
Using the unfolded state as the reference state improves the performance of statistical potentials. PMID:23199923
New pockets in dengue virus 2 surface identified by molecular dynamics simulation. PMID:23197323
PTMcode: a database of known and predicted functional associations between post-translational modifications in proteins. PMID:23193284
The RCSB Protein Data Bank: new resources for research and education. PMID:23193259
A solvated ligand rotamer approach and its application in computational protein design. PMID:23192355
Prediction of protein-destabilizing polymorphisms by manual curation with protein structure. PMID:23189203
Myosinome: a database of myosins from select eukaryotic genomes to facilitate analysis of sequence-structure-function relationships. PMID:23189029
eThread: a highly optimized machine learning-based approach to meta-threading and the modeling of protein tertiary structures. PMID:23185577
Insights into the structure, correlated motions, and electrostatic properties of two HIV-1 gp120 V3 loops. PMID:23185486
Kinetic characterization of the critical step in HIV-1 protease maturation. PMID:23184967
An artificial neural network approach to improving the correlation between protein energetics and the backbone structure. PMID:23184572
Comparative analysis of 126 cyanobacterial genomes reveals evidence of functional diversity among homologs of the redox-regulated CP12 protein. PMID:23184231
Assessing the chemical accuracy of protein structures via peptide acidity. PMID:23182463
Novel route to chaetomellic acid A and analogues: serendipitous discovery of a more competent FTase inhibitor. PMID:23182215
Vivaldi: visualization and validation of biomacromolecular NMR structures from the PDB. PMID:23180575
Interaction between shrimp and white spot syndrome virus through PmRab7-VP28 complex: an insight using simulation and docking studies. PMID:23179770
Structural insight into inhibitor of apoptosis proteins recognition by a potent divalent smac-mimetic. PMID:23166698
3D structure analysis of PAKs: A clue to the rational design for affinity reagents and blockers. PMID:23162739
Voronoia4RNA--a database of atomic packing densities of RNA structures and their complexes. PMID:23161674
Solution NMR structure of the helicase associated domain BVU_0683(627-691) from Bacteroides vulgatus provides first structural coverage for protein domain family PF03457 and indicates domain binding to DNA. PMID:23160728
Probabilistic prediction of contacts in protein-ligand complexes. PMID:23155467
Modeling and molecular dynamics of HPA-1a and -1b polymorphisms: effects on the structure of the β3 subunit of the αIIbβ3 integrin. PMID:23155369
Coarse-grained prediction of RNA loop structures. PMID:23144887
An integrated computational approach to rationalize the activity of non-zinc-binding MMP-2 inhibitors. PMID:23144829
Structural characterization of a flavonoid glycosyltransferase from Withania somnifera. PMID:23144555
Structural mechanisms of allostery and autoinhibition in JNK family kinases. PMID:23142346
Effective inter-residue contact definitions for accurate protein fold recognition. PMID:23140471
Arginine and Lysine interactions with π residues in metalloproteins. PMID:23139592
The role of electrostatic interactions on klentaq1 insight for domain separation. PMID:23136465
Novel conformation of an RNA structural switch. PMID:23134175
The genome of the obligate intracellular parasite Trachipleistophora hominis: new insights into microsporidian genome dynamics and reductive evolution. PMID:23133373
USRCAT: real-time ultrafast shape recognition with pharmacophoric constraints. PMID:23131020
The crystallographic structure of Panicum Mosaic Virus (PMV). PMID:23123270
Nuclear magnetic resonance solution structure of an N(2)-guanine DNA adduct derived from the potent tumorigen dibenzo[a,l]pyrene: intercalation from the minor groove with ruptured Watson-Crick base pairing. PMID:23121427
Exploring the PDE5 H-pocket by ensemble docking and structure-based design and synthesis of novel β-carboline derivatives. PMID:23117589
Solvent-free synthesis, DNA-topoisomerase II activity and molecular docking study of new asymmetrically N,N'-substituted ureas. PMID:23117429
Enzyme informatics. PMID:23116471
Calculating standard reduction potentials of [4Fe-4S] proteins. PMID:23115132
A rule-based algorithm for automatic bond type perception. PMID:23113939
Rational prediction with molecular dynamics for hit identification. PMID:23110535
Accurate prediction of protein catalytic residues by side chain orientation and residue contact density. PMID:23110141
A flexible docking approach for prediction of T cell receptor-peptide-MHC complexes. PMID:23109003
When a domain is not a domain, and why it is important to properly filter proteins in databases: conflicting definitions and fold classification systems for structural domains make filtering of such databases imperative. PMID:23108912
Dynamics of heme complexed with human serum albumin: a theoretical approach. PMID:23104623
Glycan fragment database: a database of PDB-based glycan 3D structures. PMID:23104379
On the origin of influenza A hemagglutinin. PMID:23100797
High-Throughput parallel blind Virtual Screening using BINDSURF. PMID:23095663
Bacterial and fungal chitinase chiJ orthologs evolve under different selective constraints following horizontal gene transfer. PMID:23095575
IUPHAR-DB: updated database content and new features. PMID:23087376
Structural characterization of a unique interface between carbohydrate response element-binding protein (ChREBP) and 14-3-3β protein. PMID:23086940
Interrelationship between HIV-1 fitness and mutation rate. PMID:23084856
Evolutionarily consistent families in SCOP: sequence, structure and function. PMID:23078280
Interactome-wide prediction of protein-protein binding sites reveals effects of protein sequence variation in Arabidopsis thaliana. PMID:23077539
Can the energy gap in the protein-ligand binding energy landscape be used as a descriptor in virtual ligand screening? PMID:23071584
Popular computational methods to assess multiprotein complexes derived from label-free affinity purification and mass spectrometry (AP-MS) experiments. PMID:23071097
Predicting the accuracy of multiple sequence alignment algorithms by using computational intelligent techniques. PMID:23066102
Benzimidazole inhibitors of the protein kinase CHK2: clarification of the binding mode by flexible side chain docking and protein-ligand crystallography. PMID:23058106
Structural characterization of bacterioferritin from Blastochloris viridis. PMID:23056552
Independent effects of protein core size and expression on residue-level structure-evolution relationships. PMID:23056364
BioFET-SIM web interface: implementation and two applications. PMID:23056201
Integrating constitutive gene expression and chemoactivity: mining the NCI60 anticancer screen. PMID:23056181
Interpretation of the consequences of mutations in protein kinases: combined use of bioinformatics and text mining. PMID:23055974
Ubiquitin dynamics in complexes reveal molecular recognition mechanisms beyond induced fit and conformational selection. PMID:23055911
Isoniazid and thioacetazone may exhibit antitubercular activity by binding directly with the active site of mycolic acid cyclopropane synthase: Hypothesis based on computational analysis. PMID:23055630
E-Pharmacophore mapping and docking studies on Vitamin D receptor (VDR). PMID:23055614
Sequence, structure, and evolution of cellulases in glycoside hydrolase family 48. PMID:23055526
Membrane curvature protein exhibits interdomain flexibility and binds a small GTPase. PMID:23055524
Structural insight into the mode of interactions of SoxL from Allochromatium vinosum in the global sulfur oxidation cycle. PMID:23053932
An Efficient Method to Evaluate Intermolecular Interaction Energies in Large Systems Using Overlapping Multicenter ONIOM and the Fragment Molecular Orbital Method. PMID:23050059
Structural and functional characterization of the protein kinase Mps1 in Arabidopsis thaliana. PMID:23049844
Single amino acid substitutions in the chemotactic sequence of urokinase receptor modulate cell migration and invasion. PMID:23049759
Modulating testosterone pathway: a new strategy to tackle male skin aging? PMID:23049247
ASTRO-FOLD 2.0: an Enhanced Framework for Protein Structure Prediction. PMID:23049093
Predicting protein residue-residue contacts using deep networks and boosting. PMID:23047561
A nonredundant structure dataset for benchmarking protein-RNA computational docking. PMID:23047523
Literature mining of protein-residue associations with graph rules learned through distant supervision. PMID:23046792
A novel neural response algorithm for protein function prediction. PMID:23046521
Inferences from structural comparison: flexibility, secondary structure wobble and sequence alignment optimization. PMID:23046301
Three enhancements to the inference of statistical protein-DNA potentials. PMID:23042633
MESSA: MEta-Server for protein Sequence Analysis. PMID:23031578
When the lowest energy does not induce native structures: parallel minimization of multi-energy values by hybridizing searching intelligences. PMID:23028708
Coupling between catalytic loop motions and enzyme global dynamics. PMID:23028297
The future of the Protein Data Bank. PMID:23023942
Studying and polishing the PDB's macromolecules. PMID:23023928
Structure-based prediction of protein-protein interactions on a genome-wide scale. PMID:23023127
Differentiating enantioselective actions of GABOB: a possible role for threonine 244 in the binding site of GABA(C) ρ(1) receptors. PMID:23019493
Synthesis and in silico screening of a library of β-carboline-containing compounds. PMID:23019432
Relaxation estimation of RMSD in molecular dynamics immunosimulations. PMID:23019425
The use of glycoinformatics in glycochemistry. PMID:23015842
Correlating protein hot spot surface analysis using ProBiS with simulated free energies of protein-protein interfacial residues. PMID:23009716
Structural attributes for the recognition of weak and anomalous regions in coiled-coils of myosins and other motor proteins. PMID:23009691
Comparative study of enzyme activity and heme reactivity in Drosophila melanogaster and Homo sapiens cystathionine β-synthases. PMID:23002992
The description of protein internal motions aids selection of ligand binding poses by the INPHARMA method. PMID:23001323
Quality assessment of protein model-structures based on structural and functional similarities. PMID:22998498
Enhancing the volume and the optical quality of hen egg-white lysozyme crystals by coupling the salt concentration gradient crystallization method with a magnetic field. PMID:22997475
Comparative Genome Sequence Analysis Reveals the Extent of Diversity and Conservation for Glycan-Associated Proteins in Burkholderia spp. PMID:22991502
Identification of novel human dipeptidyl peptidase-IV inhibitors of natural origin (part I): virtual screening and activity assays. PMID:22984596
Computational design of a Diels-Alderase from a thermophilic esterase: the importance of dynamics. PMID:22983490
Integrating the puzzle pieces: the current atomistic picture of phospholipid-G protein coupled receptor interactions. PMID:22982815
Identification of ligand templates using local structure alignment for structure-based drug design. PMID:22978550
Identification of motions in membrane proteins by elastic network models and their experimental validation. PMID:22976035
Automatic classification of protein structures relying on similarities between alignments. PMID:22974051
Pyoverdine, the Major Siderophore in Pseudomonas aeruginosa, Evades NGAL Recognition. PMID:22973307
Toward optimal fragment generations for ab initio protein structure assembly. PMID:22972754
PPM: a side-chain and backbone chemical shift predictor for the assessment of protein conformational ensembles. PMID:22972619
The receptor-dependent LQTA-QSAR: application to a set of trypanothione reductase inhibitors. PMID:22972559
The enzymatic and metabolic capabilities of early life. PMID:22970111
Creating a community resource for protein science. PMID:22969036
Modeling coding-sequence evolution within the context of residue solvent accessibility. PMID:22967129
Protein-DNA docking with a coarse-grained force field. PMID:22966980
A system-level investigation into the mechanisms of Chinese Traditional Medicine: Compound Danshen Formula for cardiovascular disease treatment. PMID:22962593
LocTree2 predicts localization for all domains of life. PMID:22962467
Side-chain rotamer changes upon ligand binding: common, crucial, correlate with entropy and rearrange hydrogen bonding. PMID:22962462
Evolution of genes involved in gamete interaction: evidence for positive selection, duplications and losses in vertebrates. PMID:22957080
GENCODE: the reference human genome annotation for The ENCODE Project. PMID:22955987
Structure-based design of highly selective β-secretase inhibitors: synthesis, biological evaluation, and protein-ligand X-ray crystal structure. PMID:22954357
New insights on the sialidase protein family revealed by a phylogenetic analysis in metazoa. PMID:22952925
Versatility and invariance in the evolution of homologous heteromeric interfaces. PMID:22952442
Novel aromatase inhibitors by structure-guided design. PMID:22951074
Crystallization and preliminary X-ray crystallographic analysis of the putative NADP(H)-dependent oxidoreductase YncB from Vibrio vulnificus. PMID:22949204
Naphthol radical couplings determine structural features and enantiomeric excess of dalesconols in Daldinia eschscholzii. PMID:22948821
TFinDit: transcription factor-DNA interaction data depository. PMID:22943312
Assignment of protein sequences to existing domain and family classification systems: Pfam and the PDB. PMID:22942020
FunSAV: predicting the functional effect of single amino acid variants using a two-stage random forest model. PMID:22937107
The Coherent X-ray Imaging Data Bank. PMID:22936162
Producing high-accuracy lattice models from protein atomic coordinates including side chains. PMID:22934109
Inhibition of bacterial dihydrofolate reductase by 6-alkyl-2,4-diaminopyrimidines. PMID:22930550
Assessing protein conformational sampling methods based on bivariate lag-distributions of backbone angles. PMID:22926831
HSPIR: a manually annotated heat shock protein information resource. PMID:22923302
Pyruvate kinase M2 activators promote tetramer formation and suppress tumorigenesis. PMID:22922757
Identifying the hotspots on the top faces of WD40-repeat proteins from their primary sequences by β-bulges and DHSW tetrads. PMID:22916195
The landscape of the prion protein's structural response to mutation revealed by principal component analysis of multiple NMR ensembles. PMID:22912570
Intrinsic disorder in the human spliceosomal proteome. PMID:22912569
Using catalytic atom maps to predict the catalytic functions present in enzyme active sites. PMID:22909276
A bioinformatic strategy for the detection, classification and analysis of bacterial autotransporters. PMID:22905239
Predicting HLA class I non-permissive amino acid residues substitutions. PMID:22905104
Subtypes of associated protein-DNA (Transcription Factor-Transcription Factor Binding Site) patterns. PMID:22904079
Probing the peripheral site of human butyrylcholinesterase. PMID:22901043
Strategic protein target analysis for developing drugs to stop dental caries. PMID:22899687
Computational models for large-scale simulations of facilitated diffusion. PMID:22892851
B-Pred, a structure based B-cell epitopes prediction server. PMID:22888263
BioJava: an open-source framework for bioinformatics in 2012. PMID:22877863
13C NMR reveals no evidence of n-π* interactions in proteins. PMID:22876300
Kinetics and thermodynamics of 1-anilino-8-naphthalene sulfonate interactions with Urinary Trypsin Inhibitor. PMID:22875404
Association of HLA-DR1 with the allergic response to the major mugwort pollen allergen: molecular background. PMID:22871092
Structure determination by multiple-wavelength anomalous dispersion (MAD) at the Pr LIII edge. PMID:22869138
Spectroscopy and speciation studies on the interactions of aluminum (III) with ciprofloxacin and β-nicotinamide adenine dinucleotide phosphate in aqueous solutions. PMID:22864244
The methionine-aromatic motif plays a unique role in stabilizing protein structure. PMID:22859300
Rationalization of paclitaxel insensitivity of yeast β-tubulin and human βIII-tubulin isotype using principal component analysis. PMID:22849332
Sequencing of seven haloarchaeal genomes reveals patterns of genomic flux. PMID:22848480
Scale-free behaviour of amino acid pair interactions in folded proteins. PMID:22848462
Profiling lipid-protein interactions using nonquenched fluorescent liposomal nanovesicles and proteome microarrays. PMID:22843995
Computational modeling of the bHLH domain of the transcription factor TWIST1 and R118C, S144R and K145E mutants. PMID:22839202
BetaSearch: a new method for querying β-residue motifs. PMID:22839199
Sequence and structural analyses of nuclear export signals in the NESdb database. PMID:22833565
Coexistence of phases in a protein heterodimer. PMID:22830730
A probabilistic fragment-based protein structure prediction algorithm. PMID:22829868
Comparison and correlation of binding mode of ATP in the kinase domains of Hexokinase family. PMID:22829728
Homology modelling of CB1 receptor and selection of potential inhibitor against Obesity. PMID:22829723
ACPYPE - AnteChamber PYthon Parser interfacE. PMID:22824207
Defining and searching for structural motifs using DeepView/Swiss-PdbViewer. PMID:22823337
A strategy based on protein-protein interface motifs may help in identifying drug off-targets. PMID:22817115
Simulating molecular mechanisms of the MDM2-mediated regulatory interactions: a conformational selection model of the MDM2 lid dynamics. PMID:22815859
Identification of potential small molecule binding pockets on Rho family GTPases. PMID:22815826
Protein surface matching by combining local and global geometric information. PMID:22815760
Template-based protein structure modeling using the RaptorX web server. PMID:22814390
A chemical group graph representation for efficient high-throughput analysis of atomistic protein simulations. PMID:22809421
P.R.E.S.S.--an R-package for exploring residual-level protein structural statistics. PMID:22809383
Recursive protein modeling: a divide and conquer strategy for Protein Structure Prediction and its case study in CASP9. PMID:22809379
Putting proteins in context: scientific illustrations bring together information from diverse sources to provide an integrative view of the molecular biology of cells. PMID:22806423
Taxifolin suppresses UV-induced skin carcinogenesis by targeting EGFR and PI3K. PMID:22805054
Crystal and NMR structures of a Trp-cage mini-protein benchmark for computational fold prediction. PMID:22802678
Integrative structural modeling with small angle X-ray scattering profiles. PMID:22800408
Re-visiting protein-centric two-tier classification of existing DNA-protein complexes. PMID:22800292
Insight into the structure, dynamics and the unfolding property of amylosucrases: implications of rational engineering on thermostability. PMID:22792323
Druggability analysis and structural classification of bromodomain acetyl-lysine binding sites. PMID:22788793
Structural basis of LaDR5, a novel agonistic anti-death receptor 5 (DR5) monoclonal antibody, to inhibit DR5/TRAIL complex formation. PMID:22788777
Identification of a functionally critical GXXG motif and its relationship to the folate binding site of the proton-coupled folate transporter (PCFT-SLC46A1). PMID:22785121
Cracking the elusive alignment hypothesis: the microtubule-cellulose synthase nexus unraveled. PMID:22784824
Automated identification of protein-ligand interaction features using Inductive Logic Programming: a hexose binding case study. PMID:22783946
Computational prediction of N-linked glycosylation incorporating structural properties and patterns. PMID:22782545
IUPHAR-DB: an open-access, expert-curated resource for receptor and ion channel research. PMID:22778867
Cysteine thioesters as myelin proteolipid protein analogues to examine the role of butyrylcholinesterase in myelin decompaction. PMID:22778864
CbrA is a flavin adenine dinucleotide protein that modifies the Escherichia coli outer membrane and confers specific resistance to Colicin M. PMID:22773789
A comparison of genotype-phenotype maps for RNA and proteins. PMID:22768948
Genetic characterization of human influenza viruses in the pandemic (2009-2010) and post-pandemic (2010-2011) periods in Japan. PMID:22761651
MuSiC: identifying mutational significance in cancer genomes. PMID:22759861
On the effect of protein conformation diversity in discriminating among neutral and disease related single amino acid substitutions. PMID:22759653
Predict impact of single amino acid change upon protein structure. PMID:22759652
How to evaluate performance of prediction methods? Measures and their interpretation in variation effect analysis. PMID:22759650
IDDI: integrated domain-domain interaction and protein interaction analysis system. PMID:22759586
Modeling regionalized volumetric differences in protein-ligand binding cavities. PMID:22759583
High performance transcription factor-DNA docking with GPU computing. PMID:22759575
Protein surface representation and analysis by dimension reduction. PMID:22759567
A systematic comparison of genome-scale clustering algorithms. PMID:22759431
Combined structure-based pharmacophore and 3D-QSAR studies on phenylalanine series compounds as TPH1 inhibitors. PMID:22754301
In silico prediction of exposure amino acid sequences of outer inflammatory protein A of Helicobacter pylori for surface display on Eschierchia coli. PMID:22754227
Effect of temperature on DNA double helix: An insight from molecular dynamics simulation. PMID:22750982
Virtual target screening: validation using kinase inhibitors. PMID:22747098
Structural analysis of a peptide fragment of transmembrane transporter protein bilitranslocase. PMID:22745694
Elaidyl-sulfamide, an oleoylethanolamide-modelled PPARα agonist, reduces body weight gain and plasma cholesterol in rats. PMID:22736460
Predicting nonspecific ion binding using DelPhi. PMID:22735539
Overcoming sequence misalignments with weighted structural superposition. PMID:22733542
Residue-ligand interaction energy (ReLIE) on a receptor-dependent 3D-QSAR analysis of S- and NH-DABOs as non-nucleoside reverse transcriptase inhibitors. PMID:22732882
Public domain databases for medicinal chemistry. PMID:22731701
Microscopic modeling of charge transport in sensing proteins. PMID:22726939
eIF4E-binding protein regulation of mRNAs with differential 5'-UTR secondary structure: a polyelectrostatic model for a component of protein-mRNA interactions. PMID:22718971
Redox-mediated mechanisms regulate DNA binding activity of the G-group of basic region leucine zipper (bZIP) transcription factors in Arabidopsis. PMID:22718771
Directory of useful decoys, enhanced (DUD-E): better ligands and decoys for better benchmarking. PMID:22716043
Protein sequence alignment analysis by local covariation: coevolution statistics detect benchmark alignment errors. PMID:22715369
Comparative molecular docking analysis of essential oil constituents as elastase inhibitors. PMID:22715299
On the calculation of ³Jαβ-coupling constants for side chains in proteins. PMID:22714630
Biophysical limits of protein-ligand binding. PMID:22713103
An improved structural characterisation of reduced French bean plastocyanin based on NMR data and local-elevation molecular dynamics simulation. PMID:22706892
Application of 4D-QSAR studies to a series of raloxifene analogs and design of potential selective estrogen receptor modulators. PMID:22706372
Computational mapping reveals dramatic effect of Hoogsteen breathing on duplex DNA reactivity with formaldehyde. PMID:22705795
In silico and in vitro elucidation of BH3 binding specificity toward Bcl-2. PMID:22702834
Development of a comprehensive, validated pharmacophore hypothesis for anthrax toxin lethal factor (LF) inhibitors using genetic algorithms, Pareto scoring, and structural biology. PMID:22697455
Macromolecular structure modeling from 3D EM using VolRover 2.0. PMID:22696407
Hypervalent nonbonded interactions of a divalent sulfur atom. Implications in protein architecture and the functions. PMID:22695232
Ancient origin of the divergent forms of leucyl-tRNA synthetases in the Halobacteriales. PMID:22694720
NMR structure of lipoprotein YxeF from Bacillus subtilis reveals a calycin fold and distant homology with the lipocalin Blc from Escherichia coli. PMID:22693626
Prediction of molecular targets of cancer preventing flavonoid compounds using computational methods. PMID:22693608
Analytic markovian rates for generalized protein structure evolution. PMID:22693543
Structure and age jointly influence rates of protein evolution. PMID:22693443
BioMe: biologically relevant metals. PMID:22693222
3DTF: a web server for predicting transcription factor PWMs using 3D structure-based energy calculations. PMID:22693215
CPred: a web server for predicting viable circular permutations in proteins. PMID:22693212
SETTER: web server for RNA structure comparison. PMID:22693209
Reducing the dimensionality of the protein-folding search problem. PMID:22692765
Use of differential scanning fluorimetry to optimize the purification and crystallization of PLP-dependent enzymes. PMID:22691796
Towards 3D structure prediction of large RNA molecules: an integer programming framework to insert local 3D motifs in RNA secondary structure. PMID:22689763
SPEER-SERVER: a web server for prediction of protein specificity determining sites. PMID:22689646
MoNetFamily: a web server to infer homologous modules and module-module interaction networks in vertebrates. PMID:22689643
ETAscape: analyzing protein networks to predict enzymatic function and substrates in Cytoscape. PMID:22689386
CHARMM Additive All-Atom Force Field for Phosphate and Sulfate Linked to Carbohydrates. PMID:22685386
Conservation of complex knotting and slipknotting patterns in proteins. PMID:22685208
Improving links between literature and biological data with text mining: a case study with GEO, PDB and MEDLINE. PMID:22685160
Structure of a monomeric variant of rhodopsin kinase at 2.5 Å resolution. PMID:22684056
Structural and immunologic characterization of bovine, horse, and rabbit serum albumins. PMID:22677715
Multiscale modeling of double-helical DNA and RNA: a unification through Lie groups. PMID:22676719
PSC: protein surface classification. PMID:22669905
Flexibility in MuA transposase family protein structures: functional mapping with scanning mutagenesis and sequence alignment of protein homologues. PMID:22666413
Alternaria alternata allergen Alt a 1: a unique β-barrel protein dimer found exclusively in fungi. PMID:22664167
NASSAM: a server to search for and annotate tertiary interactions and motifs in three-dimensional structures of complex RNA molecules. PMID:22661578
Molecular modeling and active site analysis of SdiA homolog, a putative quorum sensor for Salmonella typhimurium pathogenecity reveals specific binding patterns of AHL transcriptional regulators. PMID:22660944
Genetic and structural characterization of the growth hormone gene and protein from tench, Tinca tinca. PMID:22660840
Inner- and outer-sphere metal coordination in blue copper proteins. PMID:22658756
Structural insights into the role of domain flexibility in human DNA ligase IV. PMID:22658747
Insulin-like growth factor binding proteins: a structural perspective. PMID:22654863
A computational investigation on the connection between dynamics properties of ribosomal proteins and ribosome assembly. PMID:22654657
A phylogenetic analysis of normal modes evolution in enzymes and its relationship to enzyme function. PMID:22651983
Transcription Factor DLX5 As a New Target for Promising Antitumor Agents. PMID:22649693
New Test System for Serine/Threonine Protein Kinase Inhibitors Screening: E. coli APHVIII/Pk25 design. PMID:22649658
Computer modeling of the structure and spectra of fluorescent proteins. PMID:22649601
The role of stacking interactions in complexes of proteins with adenine and Guanine fragments of ligands. PMID:22649598
A predictive model of intein insertion site for use in the engineering of molecular switches. PMID:22649521
Lessons from high-throughput protein crystallization screening: 10 years of practical experience. PMID:22646073
Ultrahigh and high resolution structures and mutational analysis of monomeric Streptococcus pyogenes SpeB reveal a functional role for the glycine-rich C-terminal loop. PMID:22645124
Extremophilic Acinetobacter strains from high-altitude lakes in Argentinean Puna: remarkable UV-B resistance and efficient DNA damage repair. PMID:22644565
Characterization and prediction of the binding site in DNA-binding proteins: improvement of accuracy by combining residue composition, evolutionary conservation and structural parameters. PMID:22641851
Balancing target flexibility and target denaturation in computational fragment-based inhibitor discovery. PMID:22641475
Super: a web server to rapidly screen superposable oligopeptide fragments from the protein data bank. PMID:22638586
Farnesyl pyrophosphate is an endogenous antagonist to ADP-stimulated P2Y₁₂ receptor-mediated platelet aggregation. PMID:22628078
Structure of the first sphingosine 1-phosphate receptor. PMID:22623751
What is the best reference state for designing statistical atomic potentials in protein structure prediction? PMID:22623012
Structural genomics plucks high-hanging membrane proteins. PMID:22622032
Selective targeting of melanoma by PEG-masked protein-based multifunctional nanoparticles. PMID:22619508
PocketAnnotate: towards site-based function annotation. PMID:22618878
A new method for evaluating the specificity of indirect readout in protein-DNA recognition. PMID:22618872
Do natural proteins differ from random sequences polypeptides? Natural vs. random proteins classification using an evolutionary neural network. PMID:22615786
Novel cruzain inhibitors for the treatment of Chagas' disease. PMID:22613098
Immune epitope database analysis resource. PMID:22610854
Exploring protein dynamics space: the dynasome as the missing link between protein structure and function. PMID:22606222
Identification of important chemical features of 11β-hydroxysteroid dehydrogenase type1 inhibitors: application of ligand based virtual screening and density functional theory. PMID:22606035
Phages and HIV-1: from display to interplay. PMID:22606007
PepSite: prediction of peptide-binding sites from protein surfaces. PMID:22600738
ProBiS-2012: web server and web services for detection of structurally similar binding sites in proteins. PMID:22600737
Mining the protein data bank to differentiate error from structural variation in clustered static structures: an examination of HIV protease. PMID:22590675
Discovery of a novel allosteric modulator of 5-HT3 receptors: inhibition and potentiation of Cys-loop receptor signaling through a conserved transmembrane intersubunit site. PMID:22589534
FTMAP: extended protein mapping with user-selected probe molecules. PMID:22589414
Prediction and comparison of Salmonella-human and Salmonella-Arabidopsis interactomes. PMID:22589098
Structure-based statistical analysis of transmembrane helices. PMID:22588483
Disruption of the Eng18B ENGase gene in the fungal biocontrol agent Trichoderma atroviride affects growth, conidiation and antagonistic ability. PMID:22586463
BRCT domains: A little more than kin, and less than kind. PMID:22584059
Intrinsic energy landscapes of amino acid side-chains. PMID:22582825
Water Diffusion In And Out Of The β-Barrel Of GFP and The Fast Maturing Fluorescent Protein, TurboGFP. PMID:22582003
Scoring protein interaction decoys using exposed residues (SPIDER): a novel multibody interaction scoring function based on frequent geometric patterns of interfacial residues. PMID:22581643
Analyzing effects of naturally occurring missense mutations. PMID:22577471
Docking performance of the glide program as evaluated on the Astex and DUD datasets: a complete set of glide SP results and selected results for a new scoring function integrating WaterMap and glide. PMID:22576241
Structure of bradavidin-C-terminal residues act as intrinsic ligands. PMID:22574129
West Nile virus T-cell ligand sequences shared with other flaviviruses: a multitude of variant sequences as potential altered peptide ligands. PMID:22573867
SPRITE and ASSAM: web servers for side chain 3D-motif searching in protein structures. PMID:22573174
Structural bioinformatics of the human spliceosomal proteome. PMID:22573172
Adventures in data citation: sorghum genome data exemplifies the new gold standard. PMID:22571506
COFACTOR: an accurate comparative algorithm for structure-based protein function annotation. PMID:22570420
H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations. PMID:22570416
Variability in docking success rates due to dataset preparation. PMID:22566074
Structural informatics, modeling, and design with an open-source Molecular Software Library (MSL). PMID:22565567
FDA approved drugs complexed to their targets: evaluating pose prediction accuracy of docking protocols. PMID:22562231
Fast learning optimized prediction methodology (FLOPRED) for protein secondary structure prediction. PMID:22562230
CENP-T proteins are conserved centromere receptors of the Ndc80 complex. PMID:22561346
Recognizing protein-ligand binding sites by global structural alignment and local geometry refinement. PMID:22560732
Arbitrary protein-protein docking targets biologically relevant interfaces. PMID:22559010
Cataloguing functionally relevant polymorphisms in gene DNA ligase I: a computational approach. PMID:22558535
L1pred: a sequence-based prediction tool for catalytic residues in enzymes with the L1-logreg classifier. PMID:22558194
Comparison of tertiary structures of proteins in protein-protein complexes with unbound forms suggests prevalence of allostery in signalling proteins. PMID:22554255
MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels. PMID:22553366
CSA: comprehensive comparison of pairwise protein structure alignments. PMID:22553365
Bioinformatics and variability in drug response: a protein structural perspective. PMID:22552919
A comparative analysis of protein targets of withdrawn cardiovascular drugs in human and mouse. PMID:22548699
The MULTICOM toolbox for protein structure prediction. PMID:22545707
AWSEM-MD: protein structure prediction using coarse-grained physical potentials and bioinformatically based local structure biasing. PMID:22545654
Development and validation of an improved algorithm for overlaying flexible molecules. PMID:22538643
A graph-theoretic approach for classification and structure prediction of transmembrane β-barrel proteins. PMID:22537300
Intuitive representation of surface properties of biomolecules using BioBlender. PMID:22536962
Combining automated peak tracking in SAR by NMR with structure-based backbone assignment from 15N-NOESY. PMID:22536902
Exploring functionally related enzymes using radially distributed properties of active sites around the reacting points of bound ligands. PMID:22536854
Antifungal effect of 4-arylthiosemicarbazides against Candida species. Search for molecular basis of antifungal activity of thiosemicarbazide derivatives. PMID:22535361
HD-RNAS: An Automated Hierarchical Database of RNA Structures. PMID:22529851
Cloning, expression, purification and characterization of UMP kinase from Staphylococcus aureus. PMID:22528139
Structure-based design of oxygen-linked macrocyclic kinase inhibitors: discovery of SB1518 and SB1578, potent inhibitors of Janus kinase 2 (JAK2) and Fms-like tyrosine kinase-3 (FLT3). PMID:22527961
Virtual screening using a conformationally flexible target protein: models for ligand binding to p38α MAPK. PMID:22527960
Hydroxybutyrate prevents protein aggregation in the halotolerant bacterium Pseudomonas sp. CT13 under abiotic stress. PMID:22527039
Computational models of protein kinematics and dynamics: beyond simulation. PMID:22524225
A Siglec-like sialic-acid-binding motif revealed in an adenovirus capsid protein. PMID:22522600
An analysis of B-cell epitope discontinuity. PMID:22520973
A highly selective Hsp90 affinity chromatography resin with a cleavable linker. PMID:22520629
Adapting federated cyberinfrastructure for shared data collection facilities in structural biology. PMID:22514186
Classifying and assembling two-dimensional X-ray laser diffraction patterns of a single particle to reconstruct the three-dimensional diffraction intensity function: resolution limit due to the quantum noise. PMID:22514069
Structural basis for type VI secretion effector recognition by a cognate immunity protein. PMID:22511866
Efficacy of a non-hypercalcemic vitamin-D2 derived anti-cancer agent (MT19c) and inhibition of fatty acid synthesis in an ovarian cancer xenograft model. PMID:22509304
High-throughput biological small-angle X-ray scattering with a robotically loaded capillary cell. PMID:22509071
Antimalarial activity of the anticancer histone deacetylase inhibitor SB939. PMID:22508312
Use of noncrystallographic symmetry for automated model building at medium to low resolution. PMID:22505265
Exploiting structure similarity in refinement: automated NCS and target-structure restraints in BUSTER. PMID:22505257
Three-dimensional RNA structure refinement by hydroxyl radical probing. PMID:22504587
Develop and test a solvent accessible surface area-based model in conformational entropy calculations. PMID:22497310
Modeling of the N-glycosylated transferrin receptor suggests how transferrin binding can occur within the surface coat of Trypanosoma brucei. PMID:22496646
A human ubiquitin conjugating enzyme (E2)-HECT E3 ligase structure-function screen. PMID:22496338
CheShift-2: graphic validation of protein structures. PMID:22495749
BacterialLectinDb: An integrated bacterial lectin database. PMID:22493537
PhyLAT: a phylogenetic local alignment tool. PMID:22492645
MSV3d: database of human MisSense Variants mapped to 3D protein structure. PMID:22491796
EnzyBase: a novel database for enzybiotic studies. PMID:22489867
Identification of novel liver X receptor activators by structure-based modeling. PMID:22489742
The molecular dynamics of Trypanosoma brucei UDP-galactose 4'-epimerase: a drug target for African sleeping sickness. PMID:22487100
Detection of spatial correlations in protein structures and molecular complexes. PMID:22483118
How conformational dynamics of DNA polymerase select correct substrates: experiments and simulations. PMID:22483109
Function and biotechnology of extremophilic enzymes in low water activity. PMID:22480329
CLIPS-1D: analysis of multiple sequence alignments to deduce for residue-positions a role in catalysis, ligand-binding, or protein structure. PMID:22480135
Crystal structure of Streptococcus pyogenes Csn2 reveals calcium-dependent conformational changes in its tertiary and quaternary structure. PMID:22479393
Structural insights from binding poses of CCR2 and CCR5 with clinically important antagonists: a combined in silico study. PMID:22479344
ANODE: anomalous and heavy-atom density calculation. PMID:22477786
The transcription factor encyclopedia. PMID:22458515
Evolution of a complex disease resistance gene cluster in diploid Phaseolus and tetraploid Glycine. PMID:22457424
Reductive activation of the heme iron-nitrosyl intermediate in the reaction mechanism of cytochrome c nitrite reductase: a theoretical study. PMID:22454108
IBC's 22nd Annual Antibody Engineering and 9th Annual Antibody Therapeutics International Conferences and the 2011 Annual Meeting of The Antibody Society, December 5-8, 2011, San Diego, CA. PMID:22453091
Progressive dry-core-wet-rim hydration trend in a nested-ring topology of protein binding interfaces. PMID:22452998
Roles of residues in the interface of transient protein-protein complexes before complexation. PMID:22451863
SMS 2.0: an updated database to study the structural plasticity of short peptide fragments in non-redundant proteins. PMID:22449400
Comparative proteomics reveals a significant bias toward alternative protein isoforms with conserved structure and function. PMID:22446687
Fragmentation-tree density representation for crystallographic modelling of bound ligands. PMID:22446381
A structural model of the E. coli PhoB dimer in the transcription initiation complex. PMID:22433509
Improved modeling of side-chain--base interactions and plasticity in protein--DNA interface design. PMID:22426128
An amino acid packing code for α-helical structure and protein design. PMID:22426125
Experimentally assessing molecular dynamics sampling of the protein native state conformational distribution. PMID:22425325
Predicting protein-protein interface residues using local surface structural similarity. PMID:22424103
PupDB: a database of pupylated proteins. PMID:22424087
Topological analysis and interactive visualization of biological networks and protein structures. PMID:22422314
High-throughput subtomogram alignment and classification by Fourier space constrained fast volumetric matching. PMID:22420977
phenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta. PMID:22418934
Visualisation of variable binding pockets on protein surfaces by probabilistic analysis of related structure sets. PMID:22417279
Protein misinteraction avoidance causes highly expressed proteins to evolve slowly. PMID:22416125
Fatal cases of influenza A(H3N2) in children: insights from whole genome sequence analysis. PMID:22412998
Membrane proteins, magic-angle spinning, and in-cell NMR. PMID:22411816
Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field. PMID:22411565
SMURFLite: combining simplified Markov random fields with simulated evolution improves remote homology detection for beta-structural proteins into the twilight zone. PMID:22408192
Single cycle structure-based humanization of an anti-nerve growth factor therapeutic antibody. PMID:22403636
In silico investigation of interactions between human cannabinoid receptor-1 and its antagonists. PMID:22402754
Potent antiviral HIV-1 protease inhibitor GRL-02031 adapts to the structures of drug resistant mutants with its P1'-pyrrolidinone ring. PMID:22401672
Role of wobble base pair geometry for codon degeneracy: purine-type bases at the anticodon wobble position. PMID:22399149
Rapid and accurate prediction and scoring of water molecules in protein binding sites. PMID:22396746
Degenerate T-cell recognition of peptides on MHC molecules creates large holes in the T-cell repertoire. PMID:22396638
Developing a high-quality scoring function for membrane protein structures based on specific inter-residue interactions. PMID:22395902
On docking, scoring and assessing protein-DNA complexes in a rigid-body framework. PMID:22393431
Text mining improves prediction of protein functional sites. PMID:22393388
Hexapeptide fragment of carcinoembryonic antigen which acts as an agonist of heterogeneous ribonucleoprotein M. PMID:22392880
In silico analysis of drug-resistant mutant of neuraminidase (N294S) against oseltamivir. PMID:22392098
Engineered oligomerization state of OmpF protein through computational design decouples oligomer dissociation from unfolding. PMID:22391420
The role of structural disorder in the rewiring of protein interactions through evolution. PMID:22389433
Exploring the energy landscapes of protein folding simulations with Bayesian computation. PMID:22385859
Protein-protein interactions in clathrin vesicular assembly: radial distribution of evolutionary constraints in interfaces. PMID:22384024
Structural consensus among antibodies defines the antigen binding site. PMID:22383868
Molecular docking studies of protein-nucleotide complexes using MOLSDOCK (mutually orthogonal Latin squares DOCK). PMID:22382575
Novel cGMP efflux inhibitors identified by virtual ligand screening (VLS) and confirmed by experimental studies. PMID:22380603
Cross-talk between phosphorylation and lysine acetylation in a genome-reduced bacterium. PMID:22373819
Prediction of RNA-binding amino acids from protein and RNA sequences. PMID:22373313
Non-nucleosidic inhibition of Herpes simplex virus DNA polymerase: mechanistic insights into the anti-herpetic mode of action of herbal drug withaferin A. PMID:22373101
Novel base triples in RNA structures revealed by graph theoretical searching methods. PMID:22373013
Hydration shells of molecules in molecular association: A mechanism for biomolecular recognition. PMID:22365908
Challenges in whole exome sequencing: an example from hereditary deafness. PMID:22363784
The presence of the iron-sulfur motif is important for the conformational stability of the antiviral protein, Viperin. PMID:22363738
Discovery of intramolecular signal transduction network based on a new protein dynamics model of energy dissipation. PMID:22363664
RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction. PMID:22361291
Deciphering the preference and predicting the viability of circular permutations in proteins. PMID:22359629
The S4-S5 linker acts as a signal integrator for HERG K+ channel activation and deactivation gating. PMID:22359612
HORIBALFRE program: Higher Order Residue Interactions Based ALgorithm for Fold REcognition. PMID:22355236
Glycation of calmodulin binding domain of iNOS may increase the chance of occurrence of tuberculosis in chronic diabetic state. PMID:22355231
The distribution of ligand-binding pockets around protein-protein interfaces suggests a general mechanism for pocket formation. PMID:22355140
Structure prediction of loops with fixed and flexible stems. PMID:22352982
Simultaneous single-structure and bundle representation of protein NMR structures in torsion angle space. PMID:22351031
A grid-enabled web service for low-resolution crystal structure refinement. PMID:22349228
Novel insights through the integration of structural and functional genomics data with protein networks. PMID:22343087
Worm-like Ising model for protein mechanical unfolding under the effect of osmolytes. PMID:22339871
Effects of non-nearest neighbors on the thermodynamic stability of RNA GNRA hairpin tetraloops. PMID:22329761
Structural features that predict real-value fluctuations of globular proteins. PMID:22328193
In-silico studies in Chinese herbal medicines' research: evaluation of in-silico methodologies and phytochemical data sources, and a review of research to date. PMID:22326356
Blind testing of routine, fully automated determination of protein structures from NMR data. PMID:22325772
Regulation of blood-testis barrier dynamics by desmosome, gap junction, hemidesmosome and polarity proteins: An unexpected turn of events. PMID:22319658
Comparative modeling of PON2 and analysis of its substrate binding interactions using computational methods. PMID:22319641
Computational insights for the discovery of non-ATP competitive inhibitors of MAP kinases. PMID:22316156
Investigation of D₂ receptor-agonist interactions using a combination of pharmacophore and receptor homology modeling. PMID:22315215
Combining NMR ensembles and molecular dynamics simulations provides more realistic models of protein structures in solution and leads to better chemical shift prediction. PMID:22314705
Clustering of HIV-1 Subtypes Based on gp120 V3 Loop electrostatic properties. PMID:22313935
Medicago truncatula transporter database: a comprehensive database resource for M. truncatula transporters. PMID:22309450
Synthesis, docking studies and biological evaluation of benzo[b]thiophen-2-yl-3-(4-arylpiperazin-1-yl)-propan-1-one derivatives on 5-HT1A serotonin receptors. PMID:22306829
Ashwagandha derived withanone targets TPX2-Aurora A complex: computational and experimental evidence to its anticancer activity. PMID:22303466
Homology inference of protein-protein interactions via conserved binding sites. PMID:22303436
Virtual screening and evaluation of Ketol-Acid Reducto-Isomerase (KARI) as a putative drug target for Aspergillosis. PMID:22300397
Exploring biological electron transfer pathway dynamics with the Pathways plugin for VMD. PMID:22298319
Domain swapping proceeds via complete unfolding: a 19F- and 1H-NMR study of the Cyanovirin-N protein. PMID:22296296
The structural basis for substrate versatility of chloramphenicol acetyltransferase CATI. PMID:22294317
Effects of ligands on unfolding of the amyloid β-peptide central helix: mechanistic insights from molecular dynamics simulations. PMID:22291970
Uncluttered Single-Image Visualization of Vascular Structures Using GPU and Integer Programming. PMID:22291148
Enhancement of crystallization with nucleotide ligands identified by dye-ligand affinity chromatography. PMID:22286688
SynaptomeDB: an ontology-based knowledgebase for synaptic genes. PMID:22285564
Rationalization and prediction of selective decoding of pseudouridine-modified nonsense and sense codons. PMID:22282339
Molecular dynamics simulations reveal specific interactions of post-translational palmitoyl modifications with rhodopsin in membranes. PMID:22280374
Binding affinity prediction for ligands and receptors forming tautomers and ionization species: inhibition of mitogen-activated protein kinase-activated protein kinase 2 (MK2). PMID:22280316
Determinants of reactivity and selectivity in soluble epoxide hydrolase from quantum mechanics/molecular mechanics modeling. PMID:22280021
Structural and functional characterization of proteins adsorbed on hydrophilized polylactide-co-glycolide microfibers. PMID:22275823
Detecting local ligand-binding site similarity in nonhomologous proteins by surface patch comparison. PMID:22275074
Do crystal structures obviate the need for theoretical models of GPCRs for structure-based virtual screening? PMID:22275072
Validating the vitality strategy for fighting drug resistance. PMID:22275047
Putting the pieces together: integrative modeling platform software for structure determination of macromolecular assemblies. PMID:22272186
A comparative study of the second-order hydrophobic moments for globular proteins: the consensus scale of hydrophobicity and the CHARMM partial atomic charges. PMID:22272083
Structure- and sequence-based function prediction for non-homologous proteins. PMID:22270458
ProBiS-database: precalculated binding site similarities and local pairwise alignments of PDB structures. PMID:22268964
Cloning, Baeyer-Villiger biooxidations, and structures of the camphor pathway 2-oxo-Δ(3)-4,5,5-trimethylcyclopentenylacetyl-coenzyme A monooxygenase of Pseudomonas putida ATCC 17453. PMID:22267661
New inhibitor of 3-phosphoinositide dependent protein kinase-1 identified from virtual screening. PMID:22266037
Large-scale mapping of human protein interactome using structural complexes. PMID:22261719
Improving protein template recognition by using small-angle x-ray scattering profiles. PMID:22261066
Three-dimensional reconstruction of protein networks provides insight into human genetic disease. PMID:22252508
Drug design for ever, from hype to hope. PMID:22252446
Identification of novel adenosine A(2A) receptor antagonists by virtual screening. PMID:22250781
Computational fragment-based screening using RosettaLigand: the SAMPL3 challenge. PMID:22246345
Convergent evolution in structural elements of proteins investigated using cross profile analysis. PMID:22244085
Characterisation of a cell wall-anchored protein of Staphylococcus saprophyticus associated with linoleic acid resistance. PMID:22243671
Intrinsic contribution of the 2'-hydroxyl to RNA conformational heterogeneity. PMID:22242623
Classification of protein functional surfaces using structural characteristics. PMID:22238424
Predicting folding free energy changes upon single point mutations. PMID:22238268
Critical differences in HIV-1 and HIV-2 protease specificity for clinical inhibitors. PMID:22238126
Protein docking prediction using predicted protein-protein interface. PMID:22233443
Channelpedia: an integrative and interactive database for ion channels. PMID:22232598
Identification of a small molecule that modulates platelet glycoprotein Ib-von Willebrand factor interaction. PMID:22232560
Engineering a zinc binding site into the de novo designed protein DS119 with a βαβ structure. PMID:22231358
Computational protein design with explicit consideration of surface hydrophobic patches. PMID:22223219
Solution NMR structures reveal unique homodimer formation by a winged helix-turn-helix motif and provide first structures for protein domain family PF10771. PMID:22223187
Integrating bioinformatics tools to handle glycosylation. PMID:22219715
The FGGY carbohydrate kinase family: insights into the evolution of functional specificities. PMID:22215998
SNPdbe: constructing an nsSNP functional impacts database. PMID:22210871
Molecular determinants for antibody binding on group 1 house dust mite allergens. PMID:22210776
N-glycans of human protein C inhibitor: tissue-specific expression and function. PMID:22205989
Dissecting the protein-RNA interface: the role of protein surface shapes and RNA secondary structures in protein-RNA recognition. PMID:22199255
Solution NMR structures reveal a distinct architecture and provide first structures for protein domain family PF04536. PMID:22198206
Partner-aware prediction of interacting residues in protein-protein complexes from sequence data. PMID:22194998
Predicting RNA-protein interactions using only sequence information. PMID:22192482
Structural adaptation of extreme halophilic proteins through decrease of conserved hydrophobic contact surface. PMID:22192175
Detection of secondary and supersecondary structures of proteins from cryo-electron microscopy. PMID:22186625
Virtual ligand screening against comparative protein structure models. PMID:22183533
Expanding the conformational selection paradigm in protein-ligand docking. PMID:22183530
Evolutionary trace for prediction and redesign of protein functional sites. PMID:22183528
The Y-segment of novel cold dehydrin genes is conserved and codons in the PR-10 genes are under positive selection in Oxytropis (Fabaceae) from contrasting climates. PMID:22183143
Evaluation of docking performance in a blinded virtual screening of fragment-like trypsin inhibitors. PMID:22180049
Structural insights into the allosteric effects of 4EBP1 on the eukaryotic translation initiation factor eIF4E. PMID:22178476
Computational identification and experimental characterization of substrate binding determinants of nucleotide pyrophosphatase/phosphodiesterase 7. PMID:22177013
Click modification in the N6 region of A3 adenosine receptor-selective carbocyclic nucleosides for dendrimeric tethering that preserves pharmacophore recognition. PMID:22175234
Hyperdimensional analysis of amino acid pair distributions in proteins. PMID:22174733
Designing antimicrobial peptides: form follows function. PMID:22173434
Protective effects of Commiphora erythraea resin constituents against cellular oxidative damage. PMID:22169939
Lipid recognition propensities of amino acids in membrane proteins from atomic resolution data. PMID:22168953
ATPsite: sequence-based prediction of ATP-binding residues. PMID:22165846
Neighborhood properties are important determinants of temperature sensitive mutations. PMID:22164302
Protein loop closure using orientational restraints from NMR data. PMID:22161780
PSS-3D1D: an improved 3D1D profile method of protein fold recognition for the annotation of twilight zone sequences. PMID:22160493
On the page number of RNA secondary structures with pseudoknots. PMID:22159642
Giant DNA virus mimivirus encodes pathway for biosynthesis of unusual sugar 4-amino-4,6-dideoxy-D-glucose (Viosamine). PMID:22157758
Structural and functional analysis of the archaeal endonuclease Nob1. PMID:22156373
Update of the human secretoglobin (SCGB) gene superfamily and an example of 'evolutionary bloom' of androgen-binding protein genes within the mouse Scgb gene superfamily. PMID:22155607
PSS-3D1D: an improved 3D1D profile method of protein fold recognition for the annotation of twilight zone sequences. PMID:22160493
On the page number of RNA secondary structures with pseudoknots. PMID:22159642
Giant DNA virus mimivirus encodes pathway for biosynthesis of unusual sugar 4-amino-4,6-dideoxy-D-glucose (Viosamine). PMID:22157758
Structural and functional analysis of the archaeal endonuclease Nob1. PMID:22156373
Update of the human secretoglobin (SCGB) gene superfamily and an example of 'evolutionary bloom' of androgen-binding protein genes within the mouse Scgb gene superfamily. PMID:22155607
Phosphorylation in protein-protein binding: effect on stability and function. PMID:22153503
Real space refinement of crystal structures with canonical distributions of electrons. PMID:22153496
Human proteome-scale structural modeling of E2-E3 interactions exploiting interface motifs. PMID:22149024
A force field with discrete displaceable waters and desolvation entropy for hydrated ligand docking. PMID:22148468
Structure prediction and binding sites analysis of curcin protein of Jatropha curcas using computational approaches. PMID:22146985
Prediction of the Human EP1 Receptor Binding Site by Homology Modeling and Molecular Dynamics Simulation. PMID:22145106
Genomics and privacy: implications of the new reality of closed data for the field. PMID:22144881
Targeting acetylcholinesterase: identification of chemical leads by high throughput screening, structure determination and molecular modeling. PMID:22140425
Gene3D: a domain-based resource for comparative genomics, functional annotation and protein network analysis. PMID:22139938
SitEx: a computer system for analysis of projections of protein functional sites on eukaryotic genes. PMID:22139920
Crystallization of Chlorella deoxyuridine triphosphatase. PMID:22139176
Structure of d(CGGGTACCCG)4 as a four-way Holliday junction. PMID:22139153
The structure of LsrB from Yersinia pestis complexed with autoinducer-2. PMID:22139152
mGRASP enables mapping mammalian synaptic connectivity with light microscopy. PMID:22138823
PoSSuM: a database of similar protein-ligand binding and putative pockets. PMID:22135290
Synthesis and biological activities of vitamin D-like inhibitors of CYP24 hydroxylase. PMID:22133546
Prediction of protein tertiary structures using MUFOLD. PMID:22130979
RNA CoSSMos: Characterization of Secondary Structure Motifs--a searchable database of secondary structure motifs in RNA three-dimensional structures. PMID:22127861
Identification and quantification of S-nitrosylation by cysteine reactive tandem mass tag switch assay. PMID:22126794
Deciphering the Arginine-binding preferences at the substrate-binding groove of Ser/Thr kinases by computational surface mapping. PMID:22125489
Deprotonated imidodiphosphate in AMPPNP-containing protein structures. PMID:22120745
Multiscale Modeling of Functionalized Nanocarriers in Targeted Drug Delivery. PMID:22116782
Exploration of conformational transition in the aryl-binding site of human FXa using molecular dynamics simulations. PMID:22116613
Quantum mechanical studies of lincosamides. PMID:22116607
QM/MM refinement and analysis of protein bound retinoic acid. PMID:22108894
Direct-coupling analysis of residue coevolution captures native contacts across many protein families. PMID:22106262
Sequence-based classification using discriminatory motif feature selection. PMID:22102890
Approximating protein flexibility through dynamic pharmacophore models: application to fatty acid amide hydrolase (FAAH). PMID:22098169
MINAS--a database of Metal Ions in Nucleic AcidS. PMID:22096233
POPISK: T-cell reactivity prediction using support vector machines and string kernels. PMID:22085524
Conserved water-mediated H-bonding dynamics of catalytic His159 and Asp158: insight into a possible acid-base coupled mechanism in plant thiol protease. PMID:22083165
Structure-based functional design of drugs: from target to lead compound. PMID:22081357
MIPModDB: a central resource for the superfamily of major intrinsic proteins. PMID:22080560
HotRegion: a database of predicted hot spot clusters. PMID:22080558
STITCH 3: zooming in on protein-chemical interactions. PMID:22075997
SNPeffect 4.0: on-line prediction of molecular and structural effects of protein-coding variants. PMID:22075996
Structural analyses of covalent enzyme-substrate analog complexes reveal strengths and limitations of de novo enzyme design. PMID:22075445
Predicting flexible loop regions that interact with ligands: the challenge of accurate scoring. PMID:22072600
Putting into practice domain-linear motif interaction predictions for exploration of protein networks. PMID:22069443
Automated protein structure modeling in CASP9 by I-TASSER pipeline combined with QUARK-based ab initio folding and FG-MD-based structure refinement. PMID:22069036
Computational design of high-affinity epitope scaffolds by backbone grafting of a linear epitope. PMID:22061265
A geometry force field which converts low-resolution X-ray models to structures with properties found at ultra high resolution. PMID:22057834
Bilateral inhibition of HAUSP deubiquitinase by a viral interferon regulatory factor protein. PMID:22056774
TCRep 3D: an automated in silico approach to study the structural properties of TCR repertoires. PMID:22053188
Lost in folding space? Comparing four variants of the thermodynamic model for RNA secondary structure prediction. PMID:22051375
Structural and evolutionary divergence of eukaryotic protein kinases in Apicomplexa. PMID:22047078
SPINE X: improving protein secondary structure prediction by multistep learning coupled with prediction of solvent accessible surface area and backbone torsion angles. PMID:22045506
Benchmarks for flexible and rigid transcription factor-DNA docking. PMID:22044637
Minimal functional sites allow a classification of zinc sites in proteins. PMID:22043316
Evaluation of DNA Force Fields in Implicit Solvation. PMID:22043178
STRIKE: evaluation of protein MSAs using a single 3D structure. PMID:22039207
Uncovering symmetry-breaking vector and reliability order for assigning secondary structures of proteins from atomic NMR chemical shifts in amino acids. PMID:22038647
A geometric arrangement algorithm for structure determination of symmetric protein homo-oligomers from NOEs and RDCs. PMID:22035328
Structural analysis of proinsulin hexamer assembly by hydroxyl radical footprinting and computational modeling. PMID:22033917
Structure-based design of a protein immunogen that displays an HIV-1 gp41 neutralizing epitope. PMID:22033480
Structural basis for norovirus inhibition and fucose mimicry by citrate. PMID:22031945
In silico analysis of single nucleotide polymorphism (SNPs) in human β-globin gene. PMID:22028795
Near-native protein loop sampling using nonparametric density estimation accommodating sparcity. PMID:22028638
Probing pH-dependent dissociation of HdeA dimers. PMID:22026371
The Histone Database: an integrated resource for histones and histone fold-containing proteins. PMID:22025671
A photon-free approach to transmembrane protein structure determination. PMID:22024595
A new concept to reveal protein dynamics based on energy dissipation. PMID:22022616
Conservation of the human integrin-type beta-propeller domain in bacteria. PMID:22022374
Target highlights in CASP9: Experimental target structures for the critical assessment of techniques for protein structure prediction. PMID:22020785
Consensus among flexible fitting approaches improves the interpretation of cryo-EM data. PMID:22019767
NNScore 2.0: a neural-network receptor-ligand scoring function. PMID:22017367
Comparison of the structural basis for thermal stability between archaeal and bacterial proteins. PMID:22015540
Statistical potential for modeling and ranking of protein-ligand interactions. PMID:22014038
canSAR: an integrated cancer public translational research and drug discovery resource. PMID:22013161
Hydration sites of unpaired RNA bases: a statistical analysis of the PDB structures. PMID:22011380
Prediction of enzyme mutant activity using computational mutagenesis and incremental transduction. PMID:22007208
Predicting extreme pKa shifts in staphylococcal nuclease mutants with constant pH molecular dynamics. PMID:22002886
A new generation of crystallographic validation tools for the protein data bank. PMID:22000512
Computational modeling of allosteric communication reveals organizing principles of mutation-induced signaling in ABL and EGFR kinases. PMID:21998569
Using structure to explore the sequence alignment space of remote homologs. PMID:21998567
Protein stability: a single recorded mutation aids in predicting the effects of other mutations in the same amino acid site. PMID:21998155
Characterization of pathogenic germline mutations in human protein kinases. PMID:21992016
Computational prediction of heme-binding residues by exploiting residue interaction network. PMID:21991319
Understanding the structural ensembles of a highly extended disordered protein. PMID:21979461
Clustering RNA structural motifs in ribosomal RNAs using secondary structural alignment. PMID:21976732
Design and development of a peptide-based adiponectin receptor agonist for cancer treatment. PMID:21974986
Measuring and analyzing tissue specificity of human genes and protein complexes. PMID:21970702
Ligand-based autotaxin pharmacophore models reflect structure-based docking results. PMID:21967734
Predicting peptide binding affinities to MHC molecules using a modified semi-empirical scoring function. PMID:21966412
Bound water at protein-protein interfaces: partners, roles and hydrophobic bubbles as a conserved motif. PMID:21961043
Structural characterization of human Uch37. PMID:21953935
Application of molecular dynamics simulations in molecular property prediction II: diffusion coefficient. PMID:21953689
Structure-guided inhibitor design for human acetyl-coenzyme A carboxylase by interspecies active site conversion. PMID:21953464
Accelerating protein docking in ZDOCK using an advanced 3D convolution library. PMID:21949741
ADAPTIVE FINITE ELEMENT MODELING TECHNIQUES FOR THE POISSON-BOLTZMANN EQUATION. PMID:21949541
Towards an integrated understanding of the structural characteristics of protein residue networks. PMID:21948188
Active-site hydration and water diffusion in cytochrome P450cam: a highly dynamic process. PMID:21943431
Improvement of structure-based potentials for protein folding by native and nonnative hydrogen bonds. PMID:21943429
Relation between molecular shape and the morphology of self-assembling aggregates: a simulation study. PMID:21943424
GTP-dependent packing of a three-helix bundle is required for atlastin-mediated fusion. PMID:21930898
Characterization of PDZ domain-peptide interaction interface based on energetic patterns. PMID:21928318
Prediction of functionally important residues in globular proteins from unusual central distances of amino acids. PMID:21923943
Generation of N-ethyl-N-nitrosourea (ENU) diabetes models in mice demonstrates genotype-specific action of glucokinase activators. PMID:21921030
Affinity of estrogens for human progesterone receptor A and B monomers and risk of breast cancer: a comparative molecular modeling study. PMID:21918635
Estimating affinities of calcium ions to proteins. PMID:21918621
Classification of heterodimer interfaces using docking models and construction of scoring functions for the complex structure prediction. PMID:21918618
Discrimination between biological interfaces and crystal-packing contacts. PMID:21918609
Charge density distributions derived from smoothed electrostatic potential functions: design of protein reduced point charge models. PMID:21915750
Structural and functional role of bases 32 and 33 in the anticodon loop of yeast mitochondrial tRNAIle. PMID:21914842
CrystalDock: a novel approach to fragment-based drug design. PMID:21910501
Improving Cry8Ka toxin activity towards the cotton boll weevil (Anthonomus grandis). PMID:21906288
Computed structures of point deletion mutants and their enzymatic activities. PMID:21905110
Ionic strength dependence of F-actin and glycolytic enzyme associations: a Brownian dynamics simulations approach. PMID:21905108
Dietary α-eleostearic acid ameliorates experimental inflammatory bowel disease in mice by activating peroxisome proliferator-activated receptor-γ. PMID:21904603
Inhibitor-bound complexes of dihydrofolate reductase-thymidylate synthase from Babesia bovis. PMID:21904052
Probing conformational states of glutaryl-CoA dehydrogenase by fragment screening. PMID:21904051
The Protein Maker: an automated system for high-throughput parallel purification. PMID:21904043
High-resolution structure prediction of a circular permutation loop. PMID:21898647
PATRIC: the comprehensive bacterial bioinformatics resource with a focus on human pathogenic species. PMID:21896772
Molecular modeling of Trypanosoma cruzi glutamate cysteine ligase and investigation of its interactions with glutathione. PMID:21894564
Characterizing protein motions from structure. PMID:21893421
Homology modeling of mosquito cytochrome P450 enzymes involved in pyrethroid metabolism: insights into differences in substrate selectivity. PMID:21892968
Predicting the effects of basepair mutations in DNA-protein complexes by thermodynamic integration. PMID:21889450
Identifying Schistosoma japonicum excretory/secretory proteins and their interactions with host immune system. PMID:21887319
AnimalLectinDb: An integrated animal lectin database. PMID:21887013
Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM. PMID:21886100
HBonanza: a computer algorithm for molecular-dynamics-trajectory hydrogen-bond analysis. PMID:21880522
In silico analysis of Pycnoporus cinnabarinus laccase active site with toxic industrial dyes. PMID:21877154
Binding free energy landscape of domain-peptide interactions. PMID:21876662
Molecular modeling approach to predict a binding mode for the complex methotrexate-carboxypeptidase G2. PMID:21866317
Development of immune-specific interaction potentials and their application in the multi-agent-system VaccImm. PMID:21858048
Comprehensive structural and substrate specificity classification of the Saccharomyces cerevisiae methyltransferome. PMID:21858014
DARS-RNP and QUASI-RNP: new statistical potentials for protein-RNA docking. PMID:21851628
In silico quest for putative drug targets in Helicobacter pylori HPAG1: molecular modeling of candidate enzymes from lipopolysaccharide biosynthesis pathway. PMID:21850571
Atomic resolution structure of EhpR: phenazine resistance in Enterobacter agglomerans Eh1087 follows principles of bleomycin/mitomycin C resistance in other bacteria. PMID:21849072
A coarse-grained force field for Protein-RNA docking. PMID:21846771
Energy design for protein-protein interactions. PMID:21842951
Identification of specificity determining residues in peptide recognition domains using an information theoretic approach applied to large-scale binding maps. PMID:21835011
Discovery of novel selective serotonin reuptake inhibitors through development of a protein-based pharmacophore. PMID:21834587
Identifying compound-target associations by combining bioactivity profile similarity search and public databases mining. PMID:21834535
Conformational changes in 2-trans-enoyl-ACP (CoA) reductase (InhA) from M. tuberculosis induced by an inorganic complex: a molecular dynamics simulation study. PMID:21833828
Catalysis by dihydrofolate reductase and other enzymes arises from electrostatic preorganization, not conformational motions. PMID:21831831
Scoring and lessons learned with the CSAR benchmark using an improved iterative knowledge-based scoring function. PMID:21830787
A novel deletion-insertion mutation identified in exon 3 of FXN in two siblings with a severe Friedreich ataxia phenotype. PMID:21830088
Benchmarking and analysis of protein docking performance in Rosetta v3.2. PMID:21829626
Direct inference of protein-DNA interactions using compressed sensing methods. PMID:21825146
Mutant alcohol dehydrogenase leads to improved ethanol tolerance in Clostridium thermocellum. PMID:21825121
Influence of solvent and intramolecular hydrogen bonding on the conformational properties of o-linked glycopeptides. PMID:21823626
Computational investigation of the binding mode of bis(hydroxylphenyl)arenes in 17β-HSD1: molecular dynamics simulations, MM-PBSA free energy calculations, and molecular electrostatic potential maps. PMID:21822722
The Phenix software for automated determination of macromolecular structures. PMID:21821126
Computational reverse-engineering of a spider-venom derived peptide active against Plasmodium falciparum SUB1. PMID:21818266
Spherical harmonics coefficients for ligand-based virtual screening of cyclooxygenase inhibitors. PMID:21818259
Polyphosphate--an ancient energy source and active metabolic regulator. PMID:21816086
Computational modeling on the recognition of the HRE motif by HIF-1: molecular docking and molecular dynamics studies. PMID:21814878
A combination of compositional index and genetic algorithm for predicting transmembrane helical segments. PMID:21814556
CONSeQuence: prediction of reference peptides for absolute quantitative proteomics using consensus machine learning approaches. PMID:21813416
Positive Darwinian selection drives the evolution of the morphology-related gene, EPCAM, in particularly species-rich lineages of African cichlid fishes. PMID:21811860
Structural conservation of druggable hot spots in protein-protein interfaces. PMID:21808046
Comprehensive, atomic-level characterization of structurally characterized protein-protein interactions: the PICCOLO database. PMID:21801404
Design of HIV-1 protease inhibitors with C3-substituted hexahydrocyclopentafuranyl urethanes as P2-ligands: synthesis, biological evaluation, and protein-ligand X-ray crystal structure. PMID:21800876
Rigorous assessment and integration of the sequence and structure based features to predict hot spots. PMID:21798070
Molecular evolution of cyclin proteins in animals and fungi. PMID:21798004
A conformation-dependent stereochemical library improves crystallographic refinement even at atomic resolution. PMID:21795811
Unraveling the high- and low-sensitivity agonist responses of nicotinic acetylcholine receptors. PMID:21795528
Reactivity of thioredoxin as a protein thiol-disulfide oxidoreductase. PMID:21793530
Computer modeling of nitroxide spin labels on proteins. PMID:21792846
Three-Dimensional Structure of Arabidopsis thaliana Lipase Predicted by Homology Modeling Method. PMID:21792274
SNOSite: exploiting maximal dependence decomposition to identify cysteine S-nitrosylation with substrate site specificity. PMID:21789187
Solution NMR structure of MED25(391-543) comprising the activator-interacting domain (ACID) of human mediator subunit 25. PMID:21785987
A molecular mechanics approach to modeling protein-ligand interactions: relative binding affinities in congeneric series. PMID:21780805
Adaptive Skin Meshes Coarsening for Biomolecular Simulation. PMID:21779137
NMR structure of a 4 x 4 nucleotide RNA internal loop from an R2 retrotransposon: identification of a three purine-purine sheared pair motif and comparison to MC-SYM predictions. PMID:21778280
The cytoplasmic rhodopsin-protein interface: potential for drug discovery. PMID:21777183
Systematic placement of structural water molecules for improved scoring of protein-ligand interactions. PMID:21771870
HelmCoP: an online resource for helminth functional genomics and drug and vaccine targets prioritization. PMID:21760913
Construction and test of ligand decoy sets using MDock: community structure-activity resource benchmarks for binding mode prediction. PMID:21755952
Structure-based prediction of methyl chemical shifts in proteins. PMID:21748266
A coarse-grained approach to protein design: learning from design to understand folding. PMID:21747930
Systematic approaches towards the development of host-directed antiviral therapeutics. PMID:21747723
Sulfotyrosine recognition as marker for druggable sites in the extracellular space. PMID:21747703
Probing for DNA damage with β-hairpins: similarities in incision efficiencies of bulky DNA adducts by prokaryotic and human nucleotide excision repair systems in vitro. PMID:21741328
The evolutionary history of the catenin gene family during metazoan evolution. PMID:21740572
Participation of protein sequence termini in crystal contacts. PMID:21739502
Synthesis and secretion of gonadotropins including structure-function correlates. PMID:21739108
Characterization of protein-protein interaction interfaces from a single species. PMID:21738603
Physicochemical characterization and functional site analysis of lactoferrin gene of Vechur cow. PMID:21738329
The selective estrogen receptor modulator bazedoxifene inhibits hormone-independent breast cancer cell growth and down-regulates estrogen receptor α and cyclin D1. PMID:21737572
An evolutionary trade-off between protein turnover rate and protein aggregation favors a higher aggregation propensity in fast degrading proteins. PMID:21731483
Characterization of a deswapped triple mutant bovine odorant binding protein. PMID:21731442
CSAR benchmark exercise of 2010: selection of the protein-ligand complexes. PMID:21728306
Temperature-induced melting of double-stranded DNA in the absence and presence of covalently bonded antitumour drugs: insight from molecular dynamics simulations. PMID:21727089
Immunogenicity of autoantigens. PMID:21726451
Important role of hydrophobic interactions in high-pressure adaptation of proteins. PMID:21725885
NMR structural inference of symmetric homo-oligomers. PMID:21718128
Identification of alternative binding sites for inhibitors of HIV-1 ribonuclease H through comparative analysis of virtual enrichment studies. PMID:21714567
The crystal structure of Streptococcus pyogenes uridine phosphorylase reveals a distinct subfamily of nucleoside phosphorylases. PMID:21707079
Consistent two-dimensional visualization of protein-ligand complex series. PMID:21702959
Homology modeling, molecular dynamics and QM/MM study of the regulatory protein PhoP from Corynebacterium pseudotuberculosis. PMID:21701810
Mutation D816V alters the internal structure and dynamics of c-KIT receptor cytoplasmic region: implications for dimerization and activation mechanisms. PMID:21698178
Anchored design of protein-protein interfaces. PMID:21698112
Non-bisphosphonate inhibitors of isoprenoid biosynthesis identified via computer-aided drug design. PMID:21696546
MetaDBSite: a meta approach to improve protein DNA-binding sites prediction. PMID:21689482
DBAC: a simple prediction method for protein binding hot spots based on burial levels and deeply buried atomic contacts. PMID:21689480
Structure-based prediction reveals capping motifs that inhibit β-helix aggregation. PMID:21685332
A method for probing the mutational landscape of amyloid structure. PMID:21685090
Sequence-based prediction of protein crystallization, purification and production propensity. PMID:21685077
Environment specific substitution tables improve membrane protein alignment. PMID:21685065
In-silico prediction of disorder content using hybrid sequence representation. PMID:21682902
HomPPI: a class of sequence homology based protein-protein interface prediction methods. PMID:21682895
Epitope prediction based on random peptide library screening: benchmark dataset and prediction tools evaluation. PMID:21681149
Structural principles within the human-virus protein-protein interaction network. PMID:21680884
PKA phosphorylation of NDE1 is DISC1/PDE4 dependent and modulates its interaction with LIS1 and NDEL1. PMID:21677187
MarkUs: a server to navigate sequence-structure-function space. PMID:21672961
Replica exchange molecular dynamics simulation of structure variation from α/4β-fold to 3α-fold protein. PMID:21670991
A comparison of four pair-wise sequence alignment methods. PMID:21670797
Backbone resonance assignment and order tensor estimation using residual dipolar couplings. PMID:21667298
SA-Mot: a web server for the identification of motifs of interest extracted from protein loops. PMID:21665924
Ligand-binding PAS domains in a genomic, cellular, and structural context. PMID:21663441
Biophysical mapping of the adenosine A2A receptor. PMID:21661720
The Conformation of the Estrogen Receptor Directs Estrogen-Induced Apoptosis in Breast Cancer: A Hypothesis. PMID:21660224
AN EFFICIENT HIGHER-ORDER FAST MULTIPOLE BOUNDARY ELEMENT SOLUTION FOR POISSON-BOLTZMANN BASED MOLECULAR ELECTROSTATICS. PMID:21660123
Identification of antifreeze proteins and their functional residues by support vector machine and genetic algorithms based on n-peptide compositions. PMID:21655262
Structure collisions between interacting proteins. PMID:21655095
Water-mediated ionic interactions in protein structures. PMID:21654080
High throughput isolation and glycosylation analysis of IgG-variability and heritability of the IgG glycome in three isolated human populations. PMID:21653738
Protein structure along the order-disorder continuum. PMID:21650183
HIVToolbox, an integrated web application for investigating HIV. PMID:21647445
Relative solvent accessible surface area predicts protein conformational changes upon binding. PMID:21645856
What's in a drop? Correlating observations and outcomes to guide macromolecular crystallization experiments. PMID:21643490
Isolation of thylakoid membrane complexes from rice by a new double-strips BN/SDS-PAGE and bioinformatics prediction of stromal ridge subunits interaction. PMID:21637806
Synthesis of all-hydrocarbon stapled α-helical peptides by ring-closing olefin metathesis. PMID:21637196
Crystal structure of the novel PaiA N-acetyltransferase from Thermoplasma acidophilum involved in the negative control of sporulation and degradative enzyme production. PMID:21633970
Crystal structure of the novel PaiB transcriptional regulator from Geobacillus stearothermophilus. PMID:21633969
Crystal structures of T. b. rhodesiense adenosine kinase complexed with inhibitor and activator: implications for catalysis and hyperactivation. PMID:21629723
An Algebro-topological description of protein domain structure. PMID:21629687
The influence of the local sequence environment on RNA loop structures. PMID:21628431
Protein-protein HADDocking using exclusively pseudocontact shifts. PMID:21626213
Crystal structure of a putative transcriptional regulator SCO0520 from Streptomyces coelicolor A3(2) reveals an unusual dimer among TetR family proteins. PMID:21625866
R3D-BLAST: a search tool for similar RNA 3D substructures. PMID:21624889
SwissDock, a protein-small molecule docking web service based on EADock DSS. PMID:21624888
Rosetta FlexPepDock web server--high resolution modeling of peptide-protein interactions. PMID:21622962
Structural basis for Aβ1–42 toxicity inhibition by Aβ C-terminal fragments: discrete molecular dynamics study. PMID:21621545
Binding ligand prediction for proteins using partial matching of local surface patches. PMID:21614188
PredUs: a web server for predicting protein interfaces using structural neighbors. PMID:21609948
Stereochemical errors and their implications for molecular dynamics simulations. PMID:21605430
GPCR-SSFE: a comprehensive database of G-protein-coupled receptor template predictions and homology models. PMID:21605354
New synthetic thrombin inhibitors: molecular design and experimental verification. PMID:21603576
CLICK--topology-independent comparison of biomolecular 3D structures. PMID:21602266
Inferring transcription factor complexes from ChIP-seq data. PMID:21602262
BUDDY-system: A web site for constructing a dataset of protein pairs between ligand-bound and unbound states. PMID:21600047
Biological insights from topology independent comparison of protein 3D structures. PMID:21596786
A multiple antibiotic and serum resistant oligotrophic strain, Klebsiella pneumoniae MB45 having novel dfrA30, is sensitive to ZnO QDs. PMID:21595893
Structure-based approach to rationally design a chimeric protein for an effective vaccine against Group B Streptococcus infections. PMID:21593422
SDM--a server for predicting effects of mutations on protein stability and malfunction. PMID:21593128
Objective identification of residue ranges for the superposition of protein structures. PMID:21592348
The role of tyrosine 71 in modulating the flap conformations of BACE1. PMID:21590744
Expression and β-glucan binding properties of Scots pine (Pinus sylvestris L.) antimicrobial protein (Sp-AMP). PMID:21584858
In silico studies on marine actinomycetes as potential inhibitors for Glioblastoma multiforme. PMID:21584184
DEPTH: a web server to compute depth and predict small-molecule binding cavities in proteins. PMID:21576233
Insights from the structural analysis of protein heterodimer interfaces. PMID:21572879
Coarse-graining the electrostatic potential via distributed multipole expansions. PMID:21572587
Non-Alignment Features Based Enzyme/Non-Enzyme Classification Using an Ensemble Method. PMID:21572553
Rosetta FlexPepDock ab-initio: simultaneous folding, docking and refinement of peptides onto their receptors. PMID:21572516
An expanded binding model for Cys2His2 zinc finger protein-DNA interfaces. PMID:21572177
Certain heptapeptide and large sequences representing an entire helix, strand or coil conformation in proteins are associated as chameleon sequences. PMID:21569793
PoPMuSiC 2.1: a web server for the estimation of protein stability changes upon mutation and sequence optimality. PMID:21569468
Exploring NMR ensembles of calcium binding proteins: perspectives to design inhibitors of protein-protein interactions. PMID:21569443
Extraction of consensus protein patterns in regions containing non-proline cis peptide bonds and their functional assessment. PMID:21569261
Crystal structures of a halophilic archaeal malate synthase from Haloferax volcanii and comparisons with isoforms A and G. PMID:21569248
Protein-protein docking on molecular models of Aspergillus niger RNase and human actin: novel target for anticancer therapeutics. PMID:21562828
Evidence for a fourteenth mtDNA-encoded protein in the female-transmitted mtDNA of marine Mussels (Bivalvia: Mytilidae). PMID:21556327
From isotropic to anisotropic side chain representations: comparison of three models for residue contact estimation. PMID:21552527
Sequence-based identification of 3D structural modules in RNA with RMDetect. PMID:21552257
Design and characterization of epitope-scaffold immunogens that present the motavizumab epitope from respiratory syncytial virus. PMID:21549714
APOLLO: a quality assessment service for single and multiple protein models. PMID:21546397
Hydrophobic pulses predict transmembrane helix irregularities and channel transmembrane units. PMID:21545751
Crystal structure of the HIV-2 neutralizing Fab fragment 7C8 with high specificity to the V3 region of gp125. PMID:21541316
ModEnzA: Accurate Identification of Metabolic Enzymes Using Function Specific Profile HMMs with Optimised Discrimination Threshold and Modified Emission Probabilities. PMID:21541071
Beyond structural genomics: computational approaches for the identification of ligand binding sites in protein structures. PMID:21537951
Rapid estimation of binding activity of influenza virus hemagglutinin to human and avian receptors. PMID:21533248
A topological framework for the computation of the HOMFLY polynomial and its application to proteins. PMID:21533239
Optimization of a cyclic peptide inhibitor of Ser/Thr phosphatase PPM1D (Wip1). PMID:21528848
Comparative genomics of the odorant-binding and chemosensory protein gene families across the Arthropoda: origin and evolutionary history of the chemosensory system. PMID:21527792
A collaborative filtering approach for protein-protein docking scoring functions. PMID:21526112
Analysis and modeling of the variable region of camelid single-domain antibodies. PMID:21525384
Interaction of nitric oxide with catalase: structural and kinetic analysis. PMID:21524057
Identification of novel, less toxic PTP-LAR inhibitors using in silico strategies: pharmacophore modeling, SADMET-based virtual screening and docking. PMID:21523550
PRICE (PRotein Interface Conservation and Energetics): a server for the analysis of protein-protein interfaces. PMID:21519818
Evolutionary origins of the estrogen signaling system: insights from amphioxus. PMID:21514383
PONDEROSA, an automated 3D-NOESY peak picking program, enables automated protein structure determination. PMID:21511715
Conjugal plasmid transfer in Streptomyces resembles bacterial chromosome segregation by FtsK/SpoIIIE. PMID:21505418
Crystallization and diffraction analysis of β-N-acetylhexosaminidase from Aspergillus oryzae. PMID:21505251
Simple physics-based analytical formulas for the potentials of mean force of the interaction of amino-acid side chains in water. V. Like-charged side chains. PMID:21500792
Simple physics-based analytical formulas for the potentials of mean force of the interaction of amino-acid side chains in water. VI. Oppositely charged side chains. PMID:21500791
The conserved Candida albicans CA3427 gene product defines a new family of proteins exhibiting the generic periplasmic binding protein structural fold. PMID:21494601
Structure-based identification of catalytic residues. PMID:21491495
The characterization of Thermotoga maritima ferritin reveals an unusual subunit dissociation behavior and efficient DNA protection from iron-mediated oxidative stress. PMID:21487935
mmView: a web-based viewer of the mmCIF format. PMID:21486459
Inhibitors of Helicobacter pylori protease HtrA found by 'virtual ligand' screening combat bacterial invasion of epithelia. PMID:21483848
Assignment of PolyProline II conformation and analysis of sequence--structure relationship. PMID:21483785
Structural models of CFTR-AMPK and CFTR-PKA interactions: R-domain flexibility is a key factor in CFTR regulation. PMID:21455600
Statistical measures on residue-level protein structural properties. PMID:21452025
Inferring physical protein contacts from large-scale purification data of protein complexes. PMID:21451165
Spectroscopic studies on TiO(2) enhanced binding of Hypocrellin B with DNA. PMID:21448702
A new approach to assess and predict the functional roles of proteins across all known structures. PMID:21445639
On the analysis of protein-protein interactions via knowledge-based potentials for the prediction of protein-protein docking. PMID:21432933
Metalloproteins and the pyrite-based origin of life: a critical assessment. PMID:21431891
Contribution of inter-subunit interactions to the thermostability of Pyrococcus furiosus citrate synthase. PMID:21424517
Assessing the fractions of tautomeric forms of the imidazole ring of histidine in proteins as a function of pH. PMID:21422292
Data-driven high-throughput prediction of the 3-D structure of small molecules: review and progress. PMID:21417267
Residue preference mapping of ligand fragments in the Protein Data Bank. PMID:21417260
A graphical method for analyzing distance restraints using residual dipolar couplings for structure determination of symmetric protein homo-oligomers. PMID:21413097
Interplay of flavin's redox states and protein dynamics: an insight from QM/MM simulations of dihydronicotinamide riboside quinone oxidoreductase 2. PMID:21410212
Unfolding of the amyloid β-peptide central helix: mechanistic insights from molecular dynamics simulations. PMID:21408230
TargetMine, an integrated data warehouse for candidate gene prioritisation and target discovery. PMID:21408081
Incorporating distant sequence features and radial basis function networks to identify ubiquitin conjugation sites. PMID:21408064
Evolutionary approach to predicting the binding site residues of a protein from its primary sequence. PMID:21402946
ePMV embeds molecular modeling into professional animation software environments. PMID:21397181
Higher order organization of human placental aromatase. PMID:21392520
Functional analysis of archaeal MBF1 by complementation studies in yeast. PMID:21392374
Development of polarizable models for molecular mechanical calculations II: induced dipole models significantly improve accuracy of intermolecular interaction energies. PMID:21391583
Structural analysis of K+ dependence in L-asparaginases from Lotus japonicus. PMID:21390508
Dynamically-driven inactivation of the catalytic machinery of the SARS 3C-like protease by the N214A mutation on the extra domain. PMID:21390281
U1A protein-stem loop 2 RNA recognition: prediction of structural differences from protein mutations. PMID:21384338
VISTA, a novel mouse Ig superfamily ligand that negatively regulates T cell responses. PMID:21383057
Quality assurance for the query and distribution systems of the RCSB Protein Data Bank. PMID:21382834
Identification of potential Leptospira phosphoheptose isomerase inhibitors through virtual high-throughput screening. PMID:21382593
Halogen bonds as orthogonal molecular interactions to hydrogen bonds. PMID:21378804
Structural analysis of heme proteins: implications for design and prediction. PMID:21371326
New insights into the GABA(A) receptor structure and orthosteric ligand binding: receptor modeling guided by experimental data. PMID:21365676
Study of protein complexes via homology modeling, applied to cysteine proteases and their protein inhibitors. PMID:21365221
The dynamics of Ca2+ ions within the solvation shell of calbindin D9k. PMID:21364983
Understanding TR binding to pMHC complexes: how does a TR scan many pMHC complexes yet preferentially bind to one. PMID:21364947
Biochemical correlation of activity of the α-dystroglycan-modifying glycosyltransferase POMGnT1 with mutations in muscle-eye-brain disease. PMID:21361872
PSI:Biology-materials repository: a biologist's resource for protein expression plasmids. PMID:21360289
Prediction of a new surface binding pocket and evaluation of inhibitors against huntingtin interacting protein 14: an insight using docking studies. PMID:21360185
Leveraging structure determination with fragment screening for infectious disease drug targets: MECP synthase from Burkholderia pseudomallei. PMID:21359640
Mapping protein interactions between Dengue virus and its human and insect hosts. PMID:21358811
Epigallocatechin-3-gallate potently inhibits the in vitro activity of hydroxy-3-methyl-glutaryl-CoA reductase. PMID:21357570
Selection and characterization of HIV-1 with a novel S68 deletion in reverse transcriptase. PMID:21357304
Meet me halfway: when genomics meets structural bioinformatics. PMID:21350909
Divergence of AMP Deaminase in the Ice Worm Mesenchytraeus solifugus (Annelida, Clitellata, Enchytraeidae). PMID:21350654
Inhibitory effect of flavonoids on mutant H-Rasp protein. PMID:21346872
Unique spectrum of activity of prosimian TRIM5alpha against exogenous and endogenous retroviruses. PMID:21345948
Identification of products of inhibition of GES-2 beta-lactamase by tazobactam by x-ray crystallography and spectrometry. PMID:21345789
Nonsynonymous substitution rate (Ka) is a relatively consistent parameter for defining fast-evolving and slow-evolving protein-coding genes. PMID:21342519
SoftWAXS: a computational tool for modeling wide-angle X-ray solution scattering from biomolecules. PMID:21339902
Energetics-based discovery of protein-ligand interactions on a proteomic scale. PMID:21338610
Electrostatic interactions mediate binding of obscurin to small ankyrin 1: biochemical and molecular modeling studies. PMID:21333652
Modeling the human intestinal mucin (MUC2) C-terminal cystine knot dimer. PMID:21318237
Analysis of Bacillus anthracis nucleoside hydrolase via in silico docking with inhibitors and molecular dynamics simulation. PMID:21318235
Characterization of the interactions between the nucleoprotein and the phosphoprotein of Henipavirus. PMID:21317293
Bacterial protein structures reveal phylum dependent divergence. PMID:21315656
An inverse docking approach for identifying new potential anti-cancer targets. PMID:21315634
Differences in the mannose oligomer specificities of the closely related lectins from Galanthus nivalis and Zea mays strongly determine their eventual anti-HIV activity. PMID:21314946
Molecular cloning and characterization of a membrane associated NAC family gene, SiNAC from foxtail millet [Setaria italica (L.) P. Beauv]. PMID:21312005
A computerized protein-protein interaction modeling study of ampicillin antibody specificity in relation to biosensor development. PMID:21311932
BINANA: a novel algorithm for ligand-binding characterization. PMID:21310640
A mathematical framework for protein structure comparison. PMID:21304929
Dr. PIAS: an integrative system for assessing the druggability of protein-protein interactions. PMID:21303559
Analysis of clinically relevant substrates of CYP2B6 enzyme by computational methods. PMID:21301907
Systematic assessment of accuracy of comparative model of proteins belonging to different structural fold classes. PMID:21301906
ModeRNA: a tool for comparative modeling of RNA 3D structure. PMID:21300639
Structure-guided antigen engineering yields pneumolysin mutants suitable for vaccination against pneumococcal disease. PMID:21296887
Systematic comparison of crystal and NMR protein structures deposited in the protein data bank. PMID:21293729
Research resource: Update and extension of a glycoprotein hormone receptors web application. PMID:21292827
The significance of chirality in drug design and development. PMID:21291399
A machine learning-based method to improve docking scoring functions and its application to drug repurposing. PMID:21291174
Fingerprint-based structure retrieval using electron density. PMID:21287628
Analysis of the peroxiredoxin family: using active-site structure and sequence information for global classification and residue analysis. PMID:21287625
Predicting protein flexibility through the prediction of local structures. PMID:21287616
FINDSITE-metal: integrating evolutionary information and machine learning for structure-based metal-binding site prediction at the proteome level. PMID:21287609
Specific binding of the pathogenic prion isoform: development and characterization of a humanized single-chain variable antibody fragment. PMID:21283753
Mechanisms of protein-ligand association and its modulation by protein mutations. PMID:21281585
A comparative study of HIV-1 and HTLV-I protease structure and dynamics reveals a conserved residue interaction network. PMID:21279524
Effects of HMGN variants on the cellular transcription profile. PMID:21278158
Eukaryote-wide sequence analysis of mitochondrial β-barrel outer membrane proteins. PMID:21272379
PubChem3D: Conformer generation. PMID:21272340
Searching the protein structure database for ligand-binding site similarities using CPASS v.2. PMID:21269480
Graphical analysis of pH-dependent properties of proteins predicted using PROPKA. PMID:21269479
Crystal structure of β-hexosaminidase B in complex with pyrimethamine, a potential pharmacological chaperone. PMID:21265544
The effect of a Pro²⁸Thr point mutation on the local structure and stability of human galactokinase enzyme-a theoretical study. PMID:21264483
Differential molecular information of maurotoxin peptide recognizing IK(Ca) and Kv1.2 channels explored by computational simulation. PMID:21262000
The MreB-like protein Mbl of Streptomyces coelicolor A3(2) depends on MreB for proper localization and contributes to spore wall synthesis. PMID:21257777
Directed evolution of the transcription factor XylS for development of improved expression systems. PMID:21255304
Coding potential of the products of alternative splicing in human. PMID:21251333
The discovery of potential acetylcholinesterase inhibitors: a combination of pharmacophore modeling, virtual screening, and molecular docking studies. PMID:21251245
The N-terminal tail of hERG contains an amphipathic α-helix that regulates channel deactivation. PMID:21249148
Three novel mutations in the ACTA2 gene in German patients with thoracic aortic aneurysms and dissections. PMID:21248741
Crystal structure of the human N-Myc downstream-regulated gene 2 protein provides insight into its role as a tumor suppressor. PMID:21247902
Gcn1 and actin binding to Yih1: implications for activation of the eIF2 kinase GCN2. PMID:21239490
A role for specific collagen motifs during wound healing and inflammatory response of fibroblasts in the teleost fish gilthead seabream. PMID:21232799
In silico study of the inhibition of DNA polymerase by a novel catalpol derivative. PMID:21229371
Protein structure databases. PMID:21225378
Symmetry-based self-assembled nanotubes constructed using native protein structures: the key role of flexible linkers. PMID:21222638
The molecular mechanism studies of chirality effect of PHA-739358 on Aurora kinase A by molecular dynamics simulation and free energy calculations. PMID:21222017
1,000 structures and more from the MCSG. PMID:21219649
Modeling single nucleotide polymorphisms in the human AKR1C1 and AKR1C2 genes: implications for functional and genotyping analyses. PMID:21217827
The structure of lombricine kinase: implications for phosphagen kinase conformational changes. PMID:21212263
Mining flexible-receptor docking experiments to select promising protein receptor snapshots. PMID:21210972
Symmetry-based self-assembled nanotubes constructed using native protein structures: the key role of flexible linkers. PMID:21222638
The molecular mechanism studies of chirality effect of PHA-739358 on Aurora kinase A by molecular dynamics simulation and free energy calculations. PMID:21222017
1,000 structures and more from the MCSG. PMID:21219649
Modeling single nucleotide polymorphisms in the human AKR1C1 and AKR1C2 genes: implications for functional and genotyping analyses. PMID:21217827
The structure of lombricine kinase: implications for phosphagen kinase conformational changes. PMID:21212263
Mining flexible-receptor docking experiments to select promising protein receptor snapshots. PMID:21210972
An ensemble of B-DNA dinucleotide geometries lead to characteristic nucleosomal DNA structure and provide plasticity required for gene expression. PMID:21208404
Systematic characterization of protein-DNA interactions. PMID:21207099
IGF1R variants associated with isolated single suture craniosynostosis. PMID:21204214
The recognition specificity of the CHD1 chromodomain with modified histone H3 peptides. PMID:21195088
Molecular mechanism by which palmitate inhibits PKR autophosphorylation. PMID:21192654
Water evaporation and conformational changes from partially solvated ubiquitin. PMID:21188070
Modeling loop entropy. PMID:21187223
Residual dipolar couplings: are multiple independent alignments always possible? PMID:21184138
Pharmacophore elucidation and molecular docking studies on 5-phenyl-1-(3-pyridyl)-1h-1,2,4-triazole-3-carboxylic acid derivatives as COX-2 inhibitors. PMID:21179343
TMPad: an integrated structural database for helix-packing folds in transmembrane proteins. PMID:21177659
Peptide signaling in the staphylococci. PMID:21174435
Nonparametric clustering for studying RNA conformations. PMID:21173460
Factors influencing protein tyrosine nitration--structure-based predictive models. PMID:21172423
Homology-based identification of capsid determinants that protect HIV1 from human TRIM5α restriction. PMID:21169362
Solution NMR structure of Apo-calmodulin in complex with the IQ motif of human cardiac sodium channel NaV1.5. PMID:21167176
Parity-violation energy of biomolecules-IV: protein secondary structure. PMID:21161387
A toll-like receptor-4-interacting surfactant protein-A-derived peptide suppresses tumor necrosis factor-α release from mouse JAWS II dendritic cells. PMID:21159752
Full protein flexibility is essential for proper hot-spot mapping. PMID:21158470
NetTurnP--neural network prediction of beta-turns by use of evolutionary information and predicted protein sequence features. PMID:21152409
Evolutionary innovations and the organization of protein functions in genotype space. PMID:21152394
Three-dimensional models of the oligomeric human asialoglycoprotein receptor (ASGP-R). PMID:21152305
Taxane pathway. PMID:21151855
An Integrated Database for Complex Protein Structure Modeling. PMID:21151784
Identification, activity and disulfide connectivity of C-di-GMP regulating proteins in Mycobacterium tuberculosis. PMID:21151497
Domains of Tra1 important for activator recruitment and transcription coactivator functions of SAGA and NuA4 complexes. PMID:21149579
Redrawing the Ramachandran plot after inclusion of hydrogen-bonding constraints. PMID:21148101
Structural basis for the oxidation of protein-bound sulfur by the sulfur cycle molybdohemo-enzyme sulfane dehydrogenase SoxCD. PMID:21147779
Structural determinants in streptococcal unsaturated glucuronyl hydrolase for recognition of glycosaminoglycan sulfate groups. PMID:21147778
Cell cycle sensing of oxidative stress in Saccharomyces cerevisiae by oxidation of a specific cysteine residue in the transcription factor Swi6p. PMID:21147769
Ligand migration in the apolar tunnel of Cerebratulus lacteus mini-hemoglobin. PMID:21147768
Inhibition of the NEMO/IKKβ association complex formation, a novel mechanism associated with the NF-κB activation suppression by Withania somnifera's key metabolite withaferin A. PMID:21143809
Probing the anticancer mechanism of prospective herbal drug Withaferin A on mammals: a case study on human and bovine proteasomes. PMID:21143798
Dynamics of a myoglobin mutant enzyme: 2D IR vibrational echo experiments and simulations. PMID:21142083
Electrostatic clustering and free energy calculations provide a foundation for protein design and optimization. PMID:21140293
Toward the estimation of the absolute quality of individual protein structure models. PMID:21134891
Nucleation. PMID:21132117
In vitro screening and structural characterization of inhibitors of the S100B-p53 interaction. PMID:21132089
iWRAP: An interface threading approach with application to prediction of cancer-related protein-protein interactions. PMID:21130772
Substrate binding and activation in the active site of cytochrome c nitrite reductase: a density functional study. PMID:21125303
On the mechanism of chloroquine resistance in Plasmodium falciparum. PMID:21124966
On the complexity of Engh and Huber refinement restraints: the angle τ as example. PMID:21123875
Computational generation inhibitor-bound conformers of p38 MAP kinase and comparison with experiments. PMID:21121046
Synthesis and biological evaluation of pyrazolo[1,5-a]-pyrimidine-containing 99mTc Nitrido radiopharmaceuticals as imaging agents for tumors. PMID:21119567
T Cell receptor clonotype influences epitope hierarchy in the CD8+ T cell response to respiratory syncytial virus infection. PMID:21118816
Molecular dynamics simulations of three protegrin-type antimicrobial peptides: interplay between charges at the termini, β-sheet structure and amphiphilic interactions. PMID:21113420
Brownian dynamics simulation of protein solutions: structural and dynamical properties. PMID:21112303
Evolution of the Kdo2-lipid A biosynthesis in bacteria. PMID:21106097
Computational methods for identifying a layered allosteric regulatory mechanism for ALS-causing mutations of Cu-Zn superoxide dismutase 1. PMID:21104697
Protein structure determination by exhaustive search of Protein Data Bank derived databases. PMID:21098306
PCDB: a database of protein conformational diversity. PMID:21097895
The catalytic aspartate is protonated in the Michaelis complex formed between trypsin and an in vitro evolved substrate-like inhibitor: a refined mechanism of serine protease action. PMID:21097875
Sampling the conformation of protein surface residues for flexible protein docking. PMID:21092317
Exploring the landscape of protein-ligand interaction energy using probabilistic approach. PMID:21091064
IUPHAR-DB: new receptors and tools for easy searching and visualization of pharmacological data. PMID:21087994
Exploring the factors determining the dynamics of different protein folds. PMID:21086444
Structural relationships in the lysozyme superfamily: significant evidence for glycoside hydrolase signature motifs. PMID:21085702
Drug resistance against HCV NS3/4A inhibitors is defined by the balance of substrate recognition versus inhibitor binding. PMID:21084633
Structure and catalysis of acylaminoacyl peptidase: closed and open subunits of a dimer oligopeptidase. PMID:21084296
N-glycosylation efficiency is determined by the distance to the C-terminus and the amino acid preceding an Asn-Ser-Thr sequon. PMID:21082725
Prediction of a new class of RNA recognition motif. PMID:21082207
Insights into metazoan evolution from Alvinella pompejana cDNAs. PMID:21080938
The Mycobacterium tuberculosis drugome and its polypharmacological implications. PMID:21079673
Steered molecular dynamics simulations of ligand-receptor interaction in lipocalins. PMID:21072508
PRIDB: a Protein-RNA interface database. PMID:21071426
A series of PDB related databases for everyday needs. PMID:21071423
PROMISCUOUS: a database for network-based drug-repositioning. PMID:21071407
The LabelHash algorithm for substructure matching. PMID:21070651
Development of a new physics-based internal coordinate mechanics force field and its application to protein loop modeling. PMID:21069716
Predicting translational diffusion of evolutionary conserved RNA structures by the nucleotide number. PMID:21068070
Recent advances in B-cell epitope prediction methods. PMID:21067544
Modulation of a GEF switch: autoinhibition of the intrinsic guanine nucleotide exchange activity of p115-RhoGEF. PMID:21064165
PharmGKB summary: very important pharmacogene information for PTGS2. PMID:21063235
SUPERFAMILY 1.75 including a domain-centric gene ontology method. PMID:21062816
Phospho.ELM: a database of phosphorylation sites--update 2011. PMID:21062810
A novel side-chain orientation dependent potential derived from random-walk reference state for protein fold selection and structure prediction. PMID:21060880
Antimicrobial peptides: primeval molecules or future drugs? PMID:21060861
Genomic differentiation between temperate and tropical Australian populations of Drosophila melanogaster. PMID:21059887
PolyQ: a database describing the sequence and domain context of polyglutamine repeats in proteins. PMID:21059684
Automated minimization of steric clashes in protein structures. PMID:21058396
Computer-aided drug design platform using PyMOL. PMID:21053052
ARABIDILLO proteins have a novel and conserved domain structure important for the regulation of their stability. PMID:21052782
Conformational dynamics data bank: a database for conformational dynamics of proteins and supramolecular protein assemblies. PMID:21051356
REPAIRtoire--a database of DNA repair pathways. PMID:21051355
ASD: a comprehensive database of allosteric proteins and modulators. PMID:21051350
ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing. PMID:21051348
On the origin of fluorescence in bacteriophytochrome infrared fluorescent proteins. PMID:21047084
Correlation to protein conformation of Wide-angle X-ray Scatter parameters. PMID:21046443
ThYme: a database for thioester-active enzymes. PMID:21045059
GPCRDB: information system for G protein-coupled receptors. PMID:21045054
Monoamine neurotransmitters as substrates for novel tick sulfotransferases, homology modeling, molecular docking, and enzyme kinetics. PMID:21043483
The RCSB Protein Data Bank: redesigned web site and web services. PMID:21036868
RBPDB: a database of RNA-binding specificities. PMID:21036867
ArachnoServer 2.0, an updated online resource for spider toxin sequences and structures. PMID:21036864
PREX: PeroxiRedoxin classification indEX, a database of subfamily assignments across the diverse peroxiredoxin family. PMID:21036863
The protein common interface database (ProtCID)--a comprehensive database of interactions of homologous proteins in multiple crystal forms. PMID:21036862
Docking validation resources: protein family and ligand flexibility experiments. PMID:21033739
IEDB-3D: structural data within the immune epitope database. PMID:21030437
Subdivision of the MDR superfamily of medium-chain dehydrogenases/reductases through iterative hidden Markov model refinement. PMID:20979641
Structural stability studies in adhesion molecules--role of cation-π interactions. PMID:20978808
Structural study of biologically significant ligands with major birch pollen allergen Betv1 by docking and molecular dynamics simulation. PMID:20978606
FAIR: A server for internal sequence repeats. PMID:20978598
Detection and alignment of 3D domain swapping proteins using angle-distance image-based secondary structural matching techniques. PMID:20976204
ExSer: A standalone tool to mine protein data bank (PDB) for secondary structural elements. PMID:20975886
BriX: a database of protein building blocks for structural analysis, modeling and design. PMID:20972210
DockAnalyse: an application for the analysis of protein-protein interactions. PMID:20969768
Phospho3D 2.0: an enhanced database of three-dimensional structures of phosphorylation sites. PMID:20965970
FragmentStore--a comprehensive database of fragments linking metabolites, toxic molecules and drugs. PMID:20965964
A bulky DNA lesion derived from a highly potent polycyclic aromatic tumorigen stabilizes nucleosome core particle structure. PMID:20964331
Novel fold and carbohydrate specificity of the potent anti-HIV cyanobacterial lectin from Oscillatoria agardhii. PMID:20961847
Analysis of binding properties and specificity through identification of the interface forming residues (IFR) for serine proteases in silico docked to different inhibitors. PMID:20961427
Impact of translational error-induced and error-free misfolding on the rate of protein evolution. PMID:20959819
Cross-reactivity virtual profiling of the human kinome by X-react(KIN): a chemical systems biology approach. PMID:20958088
Structural features governing the activity of lactoferricin-derived peptides that act in synergy with antibiotics against Pseudomonas aeruginosa in vitro and in vivo. PMID:20956602
Calculating pKa values in the cAMP-dependent protein kinase: the effect of conformational change and ligand binding. PMID:20954248
Probing the active site of the sugar isomerase domain from E. coli arabinose-5-phosphate isomerase via X-ray crystallography. PMID:20954237
Recognition of Smac-mimetic compounds by the BIR domain of cIAP1. PMID:20954235
Resveratrol, a red wine polyphenol, suppresses pancreatic cancer by inhibiting leukotriene A₄hydrolase. PMID:20952510
SuperSweet--a resource on natural and artificial sweetening agents. PMID:20952410
OMPdb: a database of {beta}-barrel outer membrane proteins from Gram-negative bacteria. PMID:20952406
Evaluation of germline BMP4 mutation as a cause of colorectal cancer. PMID:20949628
Investigating the correlations among the chemical structures, bioactivity profiles and molecular targets of small molecules. PMID:20947527
GPRC6A mediates the non-genomic effects of steroids. PMID:20947496
Computational studies of protegrin antimicrobial peptides: a review. PMID:20946928
Computational studies of colicin insertion into membranes: the closed state. PMID:20941706
Pre-calculated protein structure alignments at the RCSB PDB website. PMID:20937596
Recognition of nucleoside monophosphate substrates by Haemophilus influenzae class C acid phosphatase. PMID:20934434
Crystal structure of human interferon-λ1 in complex with its high-affinity receptor interferon-λR1. PMID:20934432
Molecular networks in drug discovery. PMID:20932236
PyETV: a PyMOL evolutionary trace viewer to analyze functional site predictions in protein complexes. PMID:20929911
MEDELLER: homology-based coordinate generation for membrane proteins. PMID:20926421
Computational analysis of HIV-1 protease protein binding pockets. PMID:20925403
Multiple templates-based homology modeling enhances structure quality of AT1 receptor: validation by molecular dynamics and antagonist docking. PMID:20924625
Activation of the edema factor of Bacillus anthracis by calmodulin: evidence of an interplay between the EF-calmodulin interaction and calcium binding. PMID:20923661
Accurate and efficient gp120 V3 loop structure based models for the determination of HIV-1 co-receptor usage. PMID:20923564
Relating the shape of protein binding sites to binding affinity profiles: is there an association? PMID:20923553
The rate of the molecular clock and the cost of gratuitous protein synthesis. PMID:20920270
A global optimization algorithm for protein surface alignment. PMID:20920230
A Drosophila model for primary coenzyme Q deficiency and dietary rescue in the developing nervous system. PMID:20889762
Evolutionary origin of a secondary structure: π-helices as cryptic but widespread insertional variations of α-helices that enhance protein functionality. PMID:20888342
Structural basis for the secretion of EvpC: a key type VI secretion system protein from Edwardsiella tarda. PMID:20886112
Insights into the binding mode and mechanism of action of some atypical retinoids as ligands of the small heterodimer partner (SHP). PMID:20882396
Constraints on HIV-1 diversity from protein structure. PMID:20881050
Promoting a structural view of biology for varied audiences: an overview of RCSB PDB resources and experiences. PMID:20877496
Applications of the Cambridge Structural Database in chemical education. PMID:20877495
Structural characterization of naturally occurring RNA single mismatches. PMID:20876693
pDOCK: a new technique for rapid and accurate docking of peptide ligands to Major Histocompatibility Complexes. PMID:20875153
Stacking and energetic contribution of aromatic islands at the binding interface of antibody proteins. PMID:20875152
SimiCon: a web tool for protein-ligand model comparison through calculation of equivalent atomic contacts. PMID:20871105
Docking to large allosteric binding sites on protein surfaces. PMID:20865533
Structural determinants of tobacco vein mottling virus protease substrate specificity. PMID:20862670
Correlated mutations: a hallmark of phenotypic amino acid substitutions. PMID:20862353
Role of Hsp70 ATPase domain intrinsic dynamics and sequence evolution in enabling its functional interactions with NEFs. PMID:20862304
Monitoring molecular-specific pharmacodynamics of rapamycin in vivo with inducible Gal4->Fluc transgenic reporter mice. PMID:20858726
SH3 domain-peptide binding energy calculations based on structural ensemble and multiple peptide templates. PMID:20856816
Predicting MHC-II binding affinity using multiple instance regression. PMID:20855923
Comprehensive structural and functional characterization of the human kinome by protein structure modeling and ligand virtual screening. PMID:20853887
The utility of geometrical and chemical restraint information extracted from predicted ligand-binding sites in protein structure refinement. PMID:20850544
NNScore: a neural-network-based scoring function for the characterization of protein-ligand complexes. PMID:20845954
Docking of the alkaloid geissospermine into acetylcholinesterase: a natural scaffold targeting the treatment of Alzheimer's disease. PMID:20844909
Predicting the disruption by UO2(2+) of a protein-ligand interaction. PMID:20842713
Computational systems chemical biology. PMID:20838980
The distinct conformational dynamics of K-Ras and H-Ras A59G. PMID:20838576
Training a scoring function for the alignment of small molecules. PMID:20831240
Determining macromolecular assembly structures by molecular docking and fitting into an electron density map. PMID:20827723
Group theory and biomolecular conformation: I. Mathematical and computational models. PMID:20827378
Isolation of mutant alginate lyases with cleavage specificity for di-guluronic acid linkages. PMID:20826807
Metal-binding sites are designed to achieve optimal mechanical and signaling properties. PMID:20826340
On catalytic preorganization in oxyanion holes: highlighting the problems with the gas-phase modeling of oxyanion holes and illustrating the need for complete enzyme models. PMID:20825150
Cheminformatics-based drug design approach for identification of inhibitors targeting the characteristic residues of MMP-13 hemopexin domain. PMID:20824169
Improved sequence-based prediction of disordered regions with multilayer fusion of multiple information sources. PMID:20823312
Mechanisms underlying dioxygen reduction in laccases. Structural and modelling studies focusing on proton transfer. PMID:20822511
Towards site-based protein functional annotations. PMID:20815142
VASP: a volumetric analysis of surface properties yields insights into protein-ligand binding specificity. PMID:20814581
Fast and accurate protein substructure searching with simulated annealing and GPUs. PMID:20813068
Solvent-induced lid opening in lipases: a molecular dynamics study. PMID:20812327
Characterizing the metabolism of Dehalococcoides with a constraint-based model. PMID:20811585
Targeting the chromosome partitioning protein ParA in tuberculosis drug discovery. PMID:20810423
Binding of protein kinase inhibitors to synapsin I inferred from pair-wise binding site similarity measurements. PMID:20808948
A structure-based approach for mapping adverse drug reactions to the perturbation of underlying biological pathways. PMID:20808786
Protein-protein docking benchmark version 4.0. PMID:20806234
Prediction of inter-residue contact clusters from hydrophobic cores. PMID:20802820
The role of the glycine triad in human glutathione synthetase. PMID:20800579
OpenHelix: bioinformatics education outside of a different box. PMID:20798181
CMASA: an accurate algorithm for detecting local protein structural similarity and its application to enzyme catalytic site annotation. PMID:20796320
Identification of ligand binding site on RXRγ using molecular docking and dynamics methods. PMID:20740296
Characterization of Prochlorococcus clades from iron-depleted oceanic regions. PMID:20733077
Mechanism of cohesin loading onto chromosomes: a conformational dynamics study. PMID:20713005
EasyModeller: A graphical interface to MODELLER. PMID:20712861
Systematic analysis of helical protein interfaces reveals targets for synthetic inhibitors. PMID:20712375
Rapid flexible docking using a stochastic rotamer library of ligands. PMID:20712341
Insights in 17beta-HSD1 enzyme kinetics and ligand binding by dynamic motion investigation. PMID:20706575
Lipidbook: a public repository for force-field parameters used in membrane simulations. PMID:20700585
Structure-based in-silico rational design of a selective peptide inhibitor for thymidine monophosphate kinase of mycobacterium tuberculosis. PMID:20697760
RNAMotifScan: automatic identification of RNA structural motifs using secondary structural alignment. PMID:20696653
Microfluidic fabrication of hydrogel microparticles containing functionalized viral nanotemplates. PMID:20695589
Virtual screening for HIV protease inhibitors: a comparison of AutoDock 4 and Vina. PMID:20694138
Purification and crystallization of human Cu/Zn superoxide dismutase recombinantly produced in the protozoan Leishmania tarentolae. PMID:20693657
Comparing interfacial dynamics in protein-protein complexes: an elastic network approach. PMID:20691107
RNA structural motifs that entail hydrogen bonds involving sugar-phosphate backbone atoms of RNA. PMID:20689681
Knotted vs. unknotted proteins: evidence of knot-promoting loops. PMID:20686683
Systematic analysis of short internal indels and their impact on protein folding. PMID:20684774
Manipulation of conformational change in proteins by single-residue perturbations. PMID:20682272
Combinations of affinity-enhancing mutations in a T cell receptor reveal highly nonadditive effects within and between complementarity determining regions and chains. PMID:20681514
Straightforward and complete deposition of NMR data to the PDBe. PMID:20680401
Comparison analysis of primary ligand-binding sites in seven-helix membrane proteins. PMID:20672377
Arabidopsis CYP72C1 is an atypical cytochrome P450 that inactivates brassinosteroids. PMID:20669042
Environment influences on the aromatic character of nucleobases and amino acids. PMID:20668897
A multifaceted study of stigma/style cysteine-rich adhesin (SCA)-like Arabidopsis lipid transfer proteins (LTPs) suggests diversified roles for these LTPs in plant growth and reproduction. PMID:20667964
Synergistic allostery, a sophisticated regulatory network for the control of aromatic amino acid biosynthesis in Mycobacterium tuberculosis. PMID:20667835
Sequence-based identification of interface residues by an integrative profile combining hydrophobic and evolutionary information. PMID:20667087
RosettaHoles2: a volumetric packing measure for protein structure refinement and validation. PMID:20665689
3D structural models of transmembrane proteins. PMID:20665277
Lead generation and optimization based on protein-ligand complementarity. PMID:20657448
Elucidating the higher-order structure of biopolymers by structural probing and mass spectrometry: MS3D. PMID:20648672
phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics. PMID:20648263
Long-range effects of histone point mutations on DNA remodeling revealed from computational analyses of SIN-mutant nucleosome structures. PMID:20647418
TASSER_low-zsc: an approach to improve structure prediction using low z-score-ranked templates. PMID:20635423
MDockPP: A hierarchical approach for protein-protein docking and its application to CAPRI rounds 15-19. PMID:20635420
Fold versus sequence effects on the driving force for protein-mediated electron transfer. PMID:20635418
Dry molten globule intermediates and the mechanism of protein unfolding. PMID:20635344
Enhanced Bounding Techniques to Reduce the Protein Conformational Search Space. PMID:20634970
A simple procedure for the derivation of electron density based surfaces of drug-receptor complexes from a combination of X-ray data and theoretical calculations. PMID:20634077
SPARTA+: a modest improvement in empirical NMR chemical shift prediction by means of an artificial neural network. PMID:20628786
Optimal network alignment with graphlet degree vectors. PMID:20628593
RKB: a Semantic Web knowledge base for RNA. PMID:20626922
A comprehensive in silico analysis of the functional and structural impact of SNPs in the IGF1R gene. PMID:20625407
PROFESS: a PROtein function, evolution, structure and sequence database. PMID:20624718
PDBWiki: added value through community annotation of the Protein Data Bank. PMID:20624717
Protein structure modelling and evaluation based on a 4-distance description of side-chain interactions. PMID:20624289
Generation of MHC class II-peptide ligands for CD4 T-cell allorecognition of MHC class II molecules. PMID:20616724
Understanding the effect of secondary structures and aggregation on human protein folding class evolution. PMID:20614111
The measured and calculated affinity of methyl- and methoxy-substituted benzoquinones for the Q(A) site of bacterial reaction centers. PMID:20607696
Predicting the accuracy of protein-ligand docking on homology models. PMID:20607693
Antibodies as a model system for comparative model refinement. PMID:20602354
Allosteric transition and binding of small molecule effectors causes curvature change in central β-sheets of selected enzymes. PMID:20602244
Structure of an archaeal non-discriminating glutamyl-tRNA synthetase: a missing link in the evolution of Gln-tRNAGln formation. PMID:20601684
Computational modeling of the potential interactions of the proteasome beta5 subunit and catechol-O-methyltransferase-resistant EGCG analogs. PMID:20596600
Automatic structure classification of small proteins using random forest. PMID:20594334
Relationship between mutation of serine residue at 315th position in M. tuberculosis catalase-peroxidase enzyme and Isoniazid susceptibility: an in silico analysis. PMID:20593210
Domain motion and interdomain hot spots in a multidomain enzyme. PMID:20589904
Beauty is in the eye of the beholder: proteins can recognize binding sites of homologous proteins in more than one way. PMID:20585553
A topological description of hubs in amino Acid interaction networks. PMID:20585353
The bridge-region of the Ku superfamily is an atypical zinc ribbon domain. PMID:20580930
Complexes of bacterial nicotinate mononucleotide adenylyltransferase with inhibitors: implication for structure-based drug design and improvement. PMID:20578699
Structural insights into the catalytic mechanism of bacterial guanosine-diphospho-D-mannose pyrophosphorylase and its regulation by divalent ions. PMID:20573954
In silico structure-function analysis of pathological variation in the HSD11B2 gene sequence. PMID:20571110
Kinome-wide interaction modelling using alignment-based and alignment-independent approaches for kinase description and linear and non-linear data analysis techniques. PMID:20569422
Impact of synchrotron radiation on macromolecular crystallography: a personal view. PMID:20567074
An effective approach for generating a three-Cys2His2 zinc-finger-DNA complex model by docking. PMID:20565873
Assemble: an interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels. PMID:20562414
Identification of the citrate-binding site of human ATP-citrate lyase using X-ray crystallography. PMID:20558738
Localization and function of the membrane-bound riboflavin in the Na+-translocating NADH:quinone oxidoreductase (Na+-NQR) from Vibrio cholerae. PMID:20558724
Protein tandem repeats - the more perfect, the less structured. PMID:20553501
Gene sequence, bioinformatics and enzymatic characterization of alpha-amylase from Saccharomycopsis fibuligera KZ. PMID:20552260
Prediction of protein-protein interactions in dengue virus coat proteins guided by low resolution cryoEM structures. PMID:20550721
MuD: an interactive web server for the prediction of non-neutral substitutions using protein structural data. PMID:20542913
PESDserv: a server for high-throughput comparison of protein binding site surfaces. PMID:20538727
A highly accurate statistical approach for the prediction of transmembrane beta-barrels. PMID:20538726
Identification of novel inhibitors for a low molecular weight protein tyrosine phosphatase via virtual screening. PMID:20538467
A generalized approach to sampling backbone conformations with RosettaDock for CAPRI rounds 13-19. PMID:20535822
Epidermis-type lipoxygenase 3 regulates adipocyte differentiation and peroxisome proliferator-activated receptor gamma activity. PMID:20530198
Discovering protein-DNA binding sequence patterns using association rule mining. PMID:20529874
dConsensus: a tool for displaying domain assignments by multiple structure-based algorithms and for construction of a consensus assignment. PMID:20529369
Shape-Dependent Global Deformation Modes of Large Protein Structures. PMID:20526444
Computational tools for the interactive exploration of proteomic and structural data. PMID:20525940
ANCHOR: a web server and database for analysis of protein-protein interaction binding pockets for drug discovery. PMID:20525787
Sub-AQUA: real-value quality assessment of protein structure models. PMID:20525730
Three-dimensional structure of beta-cell-specific zinc transporter, ZnT-8, predicted from the type 2 diabetes-associated gene variant SLC30A8 R325W. PMID:20525392
Beyond rotamers: a generative, probabilistic model of side chains in proteins. PMID:20525384
Methods of NMR structure refinement: molecular dynamics simulations improve the agreement with measured NMR data of a C-terminal peptide of GCN4-p1. PMID:20524044
deconSTRUCT: general purpose protein database search on the substructure level. PMID:20522512
Computational exploration of mobile ion distributions around RNA duplex. PMID:20518549
Diffraction techniques in structural biology. PMID:20517991
Struct2Net: a web service to predict protein-protein interactions using a structure-based approach. PMID:20513650
3DLigandSite: predicting ligand-binding sites using similar structures. PMID:20513649
Physical-chemical determinants of coil conformations in globular proteins. PMID:20512968
Molecular modeling of lanthionine synthetase component C-like protein 2: a potential target for the discovery of novel type 2 diabetes prophylactics and therapeutics. PMID:20512604
Structural and docking studies of Leucaena leucocephala Cinnamoyl CoA reductase. PMID:20512516
Crystal structure of exotype alginate lyase Atu3025 from Agrobacterium tumefaciens. PMID:20507980
PiRaNhA: a server for the computational prediction of RNA-binding residues in protein sequences. PMID:20507911
iPARTS: an improved tool of pairwise alignment of RNA tertiary structures. PMID:20507908
Conserved residue clusters at protein-protein interfaces and their use in binding site identification. PMID:20507585
New surface contacts formed upon reductive lysine methylation: improving the probability of protein crystallization. PMID:20506323
Dimerization of the hepatitis C virus nonstructural protein 4B depends on the integrity of an aminoterminal basic leucine zipper. PMID:20506268
An eScience-Bayes strategy for analyzing omics data. PMID:20504364
WIWS: a protein structure bioinformatics Web service collection. PMID:20501602
Nitration of the tumor suppressor protein p53 at tyrosine 327 promotes p53 oligomerization and activation. PMID:20499882
On the significance of an RNA tertiary structure prediction. PMID:20498460
History of biological metal utilization inferred through phylogenomic analysis of protein structures. PMID:20498051
omega-Helices in proteins. PMID:20496104
Dynamic correlation networks in human peroxisome proliferator-activated receptor-γ nuclear receptor protein. PMID:20496064
Dependency of ligand free energy landscapes on charge parameters and solvent models. PMID:20495851
Metals in proteins: cluster analysis studies. PMID:20490881
Analysis of structural water and CH···π interactions in HIV-1 protease and PTP1B complexes using a hydrogen bond prediction tool, HBPredicT. PMID:20490879
MPlot--a server to analyze and visualize tertiary structure contacts and geometrical features of helical membrane proteins. PMID:20484376
SMAP-WS: a parallel web service for structural proteome-wide ligand-binding site comparison. PMID:20484373
Griseofulvin stabilizes microtubule dynamics, activates p53 and inhibits the proliferation of MCF-7 cells synergistically with vinblastine. PMID:20482847
The Protein-DNA Interface database. PMID:20482798
A schematic model for molecular affinity and binding with Ising variables. PMID:20480964
Evolution, homology conservation, and identification of unique sequence signatures in GH19 family chitinases. PMID:20480157
ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. PMID:20478830
fpocket: online tools for protein ensemble pocket detection and tracking. PMID:20478829
3V: cavity, channel and cleft volume calculator and extractor. PMID:20478824
Binary image representation of a ligand binding site: its application to efficient sampling of a conformational ensemble. PMID:20478076
Diversity of function-related conformational changes in proteins: coordinate uncertainty, fragment rigidity, and stability. PMID:20469886
Computational protein design: validation and possible relevance as a tool for homology searching and fold recognition. PMID:20463972
GRAPE: GRaphical Abstracted Protein Explorer. PMID:20462864
GIS: a comprehensive source for protein structure similarities. PMID:20460464
FiberDock: a web server for flexible induced-fit backbone refinement in molecular docking. PMID:20460459
Analysis of substructural variation in families of enzymatic proteins with applications to protein function prediction. PMID:20459833
RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures. PMID:20459631
Spatio-temporal modeling of signaling protein recruitment to EGFR. PMID:20459599
A recombinant dromedary antibody fragment (VHH or nanobody) directed against human Duffy antigen receptor for chemokines. PMID:20458517
NCAD, a database integrating the intrinsic conformational preferences of non-coded amino acids. PMID:20455555
Real-time ligand binding pocket database search using local surface descriptors. PMID:20455259
Comparative molecular evolution of trichoderma chitinases in response to mycoparasitic interactions. PMID:20454524
Membrane catalysis of peptide-receptor binding. PMID:20453923
Accelerating electrostatic surface potential calculation with multi-scale approximation on graphics processing units. PMID:20452792
In silico analysis of sequential, structural and functional diversity of wheat cystatins and its implication in plant defense. PMID:20451161
Pleiotropic mechanisms facilitated by resveratrol and its metabolites. PMID:20450491
Structure of a monoclinic polymorph of human carbonic anhydrase II with a doubled a axis. PMID:20445238
The annotation of full zinc proteomes. PMID:20443034
SeqRate: sequence-based protein folding type classification and rates prediction. PMID:20438647
Creating PWMs of transcription factors using 3D structure-based computation of protein-DNA free binding energies. PMID:20438625
The HADDOCK web server for data-driven biomolecular docking. PMID:20431534
Activated RhoA binds to the pleckstrin homology (PH) domain of PDZ-RhoGEF, a potential site for autoregulation. PMID:20430886
PharmMapper server: a web server for potential drug target identification using pharmacophore mapping approach. PMID:20430828
Integration of open access literature into the RCSB Protein Data Bank using BioLit. PMID:20429930
Semantic integration of data on transcriptional regulation. PMID:20427517
Modeling RNA loops using sequence homology and geometric constraints. PMID:20427516
Structural fragment clustering reveals novel structural and functional motifs in alpha-helical transmembrane proteins. PMID:20420672
Predicting in vivo binding sites of RNA-binding proteins using mRNA secondary structure. PMID:20418358
A possible structural model of members of the CPF family of cuticular proteins implicating binding to components other than chitin. PMID:20417215
Optimal molecular structures of prion AGAAAAGA amyloid fibrils formatted by simulated annealing. PMID:20411399
Structural insight into substrate differentiation of the sugar-metabolizing enzyme galactitol dehydrogenase from Rhodobacter sphaeroides D. PMID:20410293
Role of water molecules in structure and energetics of Pseudomonas aeruginosa lectin I interacting with disaccharides. PMID:20410292
Detection of unrealistic molecular environments in protein structures based on expected electron densities. PMID:20405167
Ligand docking and binding site analysis with PyMOL and Autodock/Vina. PMID:20401516
Dynameomics: a comprehensive database of protein dynamics. PMID:20399180
Structural and functional analysis of the hemagglutinin-esterase of infectious salmon anaemia virus. PMID:20398710
A knowledge-guided strategy for improving the accuracy of scoring functions in binding affinity prediction. PMID:20398404
Spectroscopic and computational characterization of substrate-bound mouse cysteine dioxygenase: nature of the ferrous and ferric cysteine adducts and mechanistic implications. PMID:20397631
Why Hofmeister effects of many salts favor protein folding but not DNA helix formation. PMID:20385834
A small-molecule inhibitor of BCL6 kills DLBCL cells in vitro and in vivo. PMID:20385364
Low-complexity regions within protein sequences have position-dependent roles. PMID:20385029
Purification, crystallization and preliminary X-ray analysis of the aspartate aminotransferase of Plasmodium falciparum. PMID:20383010
Progress in rational methods of cryoprotection in macromolecular crystallography. PMID:20382989
The many twists and turns of DNA: template, telomere, tool, and target. PMID:20381338
Expression, purification and structural analysis of the Pyrococcus abyssi RNA binding protein PAB1135. PMID:20380716
Investigation of cation-π interactions in sugar-binding proteins. PMID:20379838
The evolution and functional repertoire of translation proteins following the origin of life. PMID:20377891
Protein sequences classification by means of feature extraction with substitution matrices. PMID:20377887
Alignment-free local structural search by writhe decomposition. PMID:20371498
Protein Bioinformatics Infrastructure for the Integration and Analysis of Multiple High-Throughput "omics" Data. PMID:20369061
A Stevedore's protein knot. PMID:20369018
The CATH database. PMID:20368142
Annular tautomerism: experimental observations and quantum mechanics calculations. PMID:20364360
A canonical cation-π interaction stabilizes the agonist conformation of estrogen-like nuclear receptors. PMID:20364341
Globin-like proteins in Caenorhabditis elegans: in vivo localization, ligand binding and structural properties. PMID:20361867
I-TASSER: a unified platform for automated protein structure and function prediction. PMID:20360767
The sodium/galactose symporter crystal structure is a dynamic, not so occluded state. PMID:20358053
An improved hybrid global optimization method for protein tertiary structure prediction. PMID:20357906
Structural analysis of Thermus thermophilus HB27 mannosyl-3-phosphoglycerate synthase provides evidence for a second catalytic metal ion and new insight into the retaining mechanism of glycosyltransferases. PMID:20356840
Assessing the structural conservation of protein pockets to study functional and allosteric sites: implications for drug discovery. PMID:20356358
Conformational preferences of a 14-residue fibrillogenic peptide from acetylcholinesterase. PMID:20356043
A leucine-rich repeat assembly approach for homology modeling of the human TLR5-10 and mouse TLR11-13 ectodomains. PMID:20352268
Comparing native and irradiated E. coli lactose repressor-operator complex by molecular dynamics simulation. PMID:20349312
Unusual evolution of a catalytic core element in CCA-adding enzymes. PMID:20348137
Reduced representation of protein structure: implications on efficiency and scope of detection of structural similarity. PMID:20338066
HTAPP: high-throughput autonomous proteomic pipeline. PMID:20336676
A natural missing link between activated and downhill protein folding scenarios. PMID:20336253
Structure and mutagenesis studies of the C-terminal region of licensing factor Cdt1 enable the identification of key residues for binding to replicative helicase Mcm proteins. PMID:20335175
Structure-function relationships of estrogenic triphenylethylenes related to endoxifen and 4-hydroxytamoxifen. PMID:20334368
GSK3beta: role in therapeutic landscape and development of modulators. PMID:20331603
Building macromolecular assemblies by information-driven docking: introducing the HADDOCK multibody docking server. PMID:20305088
Evolutionary constraints acting on DDX3X protein potentially interferes with Rev-mediated nuclear export of HIV-1 RNA. PMID:20300618
Efficient molecular surface rendering by linear-time pseudo-Gaussian approximation to Lee-Richards surfaces (PGALRS). PMID:20300495
Struct-NB: predicting protein-RNA binding sites using structural features. PMID:20300450
Fast automated placement of polar hydrogen atoms in protein-ligand complexes. PMID:20298519
A machine learning approach to predicting protein-ligand binding affinity with applications to molecular docking. PMID:20236947
An optimized TOPS+ comparison method for enhanced TOPS models. PMID:20236520
Conformer generation with OMEGA: algorithm and validation using high quality structures from the Protein Databank and Cambridge Structural Database. PMID:20235588
DNA architecture, deformability, and nucleosome positioning. PMID:20232929
A poxvirus Bcl-2-like gene family involved in regulation of host immune response: sequence similarity and evolutionary history. PMID:20230632
The eNMR platform for structural biology. PMID:20229048
New statistical potential for quality assessment of protein models and a survey of energy functions. PMID:20226048
The RNA backbone plays a crucial role in mediating the intrinsic stability of the GpU dinucleotide platform and the GpUpA/GpA miniduplex. PMID:20223772
X-ray crystallographic analyses of pig pancreatic alpha-amylase with limit dextrin, oligosaccharide, and alpha-cyclodextrin. PMID:20222716
Using protein-ligand docking to assess the chemical tractability of inhibiting a protein target. PMID:20221654
Density Estimation for Protein Conformation Angles Using a Bivariate von Mises Distribution and Bayesian Nonparametrics. PMID:20221312
Diffusion, crowding & protein stability in a dynamic molecular model of the bacterial cytoplasm. PMID:20221255
Elucidation of amyloid beta-protein oligomerization mechanisms: discrete molecular dynamics study. PMID:20218566
The predictive accuracy of secondary chemical shifts is more affected by protein secondary structure than solvent environment. PMID:20213252
Diversity of protein structures and difficulties in fold recognition: the curious case of protein G. PMID:20209018
Bardet-Biedl syndrome-associated small GTPase ARL6 (BBS3) functions at or near the ciliary gate and modulates Wnt signaling. PMID:20207729
Protein pockets: inventory, shape, and comparison. PMID:20205445
GASdb: a large-scale and comparative exploration database of glycosyl hydrolysis systems. PMID:20202206
Molecular mechanism of flop selectivity and subsite recognition for an AMPA receptor allosteric modulator: structures of GluA2 and GluA3 in complexes with PEPA. PMID:20199107
CARON--average RMSD of NMR structure ensembles. PMID:20198187
CytokineDB: a database collecting biological information. PMID:20198179
Universality in protein residue networks. PMID:20197043
A flexible docking scheme to explore the binding selectivity of PDZ domains. PMID:20196074
Effects of the V82A and I54V mutations on the dynamics and ligand binding properties of HIV-1 protease. PMID:20195662
Will widgets and semantic tagging change computational biology? PMID:20195550
Visualization of macromolecular structures. PMID:20195256
Visualization of multiple alignments, phylogenies and gene family evolution. PMID:20195253
Mathematical model for empirically optimizing large scale production of soluble protein domains. PMID:20193068
The Gewald multicomponent reaction. PMID:20191319
Absolute binding free energy calculations: on the accuracy of computational scoring of protein-ligand interactions. PMID:20186976
A comprehensive examination of the contributions to the binding entropy of protein-ligand complexes. PMID:20186973
Helix-sheet packing in proteins. PMID:20186972
Rapid chain tracing of polypeptide backbones in electron-density maps. PMID:20179340
Structure of the unbound form of HIV-1 subtype A protease: comparison with unbound forms of proteases from other HIV subtypes. PMID:20179334
Crystal structure of SmcR, a quorum-sensing master regulator of Vibrio vulnificus, provides insight into its regulation of transcription. PMID:20178981
Limitations of Ab initio predictions of peptide binding to MHC class II molecules. PMID:20174654
Two frequenins in Drosophila: unveiling the evolutionary history of an unusual neuronal calcium sensor (NCS) duplication. PMID:20170488
Structural and functional restraints on the occurrence of single amino acid variations in human proteins. PMID:20169194
Five-dimensional crystallography. PMID:20164643
Fast and automated functional classification with MED-SuMo: an application on purine-binding proteins. PMID:20162627
'Hot' macromolecular crystals. PMID:20161694
Exploring the contribution of collective motions to the dynamics of forced-unfolding in tubulin. PMID:20159162
Parameterization of disorder predictors for large-scale applications requiring high specificity by using an extended benchmark dataset. PMID:20158872
Bioinformatic search of plant microtubule-and cell cycle related serine-threonine protein kinases. PMID:20158871
Molecular shape and medicinal chemistry: a perspective. PMID:20158188
The Homeodomain Resource: a comprehensive collection of sequence, structure, interaction, genomic and functional information on the homeodomain protein family. PMID:20157477
AQUASOL: An efficient solver for the dipolar Poisson-Boltzmann-Langevin equation. PMID:20151727
Optimal assignment methods for ligand-based virtual screening. PMID:20150995
Fast and efficient searching of biological data resources--using EB-eye. PMID:20150321
Protein folding requires crowd control in a simulated cell. PMID:20149797
Screening of benzamidine-based thrombin inhibitors via a linear interaction energy in continuum electrostatics model. PMID:20148287
Exploring the molecular basis for selective binding of Mycobacterium tuberculosis Asp kinase toward its natural substrates and feedback inhibitors: a docking and molecular dynamics study. PMID:20140471
A survey of lambda repressor fragments from two-state to downhill folding. PMID:20138892
Functional characterization of transcription factor motifs using cross-species comparison across large evolutionary distances. PMID:20126523
Structure of bovine pancreatic ribonuclease complexed with uridine 5'-monophosphate at 1.60 A resolution. PMID:20124705
PHENIX: a comprehensive Python-based system for macromolecular structure solution. PMID:20124702
Multiple structure alignment and consensus identification for proteins. PMID:20122279
Identification of recurring protein structure microenvironments and discovery of novel functional sites around CYS residues. PMID:20122268
Comparison of PGH2 binding site in prostaglandin synthases. PMID:20122226
Mining protein dynamics from sets of crystal structures using "consensus structures". PMID:20120021
Docking flexible ligands in proteins with a solvent exposure- and distance-dependent dielectric function. PMID:20119653
JNK contributes to Hif-1alpha regulation in hypoxic neurons. PMID:20110876
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BSSF: a fingerprint based ultrafast binding site similarity search and function analysis server. PMID:20100327
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The protein kingdom extended: ordered and intrinsically disordered proteins, their folding, supramolecular complex formation, and aggregation. PMID:20097220
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DIGA--a database of improved gene annotation for phytopathogens. PMID:20089203
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TollML: a database of toll-like receptor structural motifs. PMID:20084417
SoyDB: a knowledge database of soybean transcription factors. PMID:20082720
Protein secondary structure appears to be robust under in silico evolution while protein disorder appears not to be. PMID:20081223
The proteolytic system of lactic acid bacteria revisited: a genomic comparison. PMID:20078865
Genomics, evolution, and crystal structure of a new family of bacterial spore kinases. PMID:20077512
Amino acid interaction preferences in proteins. PMID:20073083
Combining structure and sequence information allows automated prediction of substrate specificities within enzyme families. PMID:20072606
Structural and functional characterization of a novel homodimeric three-finger neurotoxin from the venom of Ophiophagus hannah (king cobra). PMID:20071329
The crystal structure and activity of a putative trypanosomal nucleoside phosphorylase reveal it to be a homodimeric uridine phosphorylase. PMID:20070944
Molecular docking and 3D-QSAR studies of HIV-1 protease inhibitors. PMID:20069323
Including Functional Annotations and Extending the Collection of Structural Classifications of Protein Loops (ArchDB). PMID:20066127
Prediction of functional class of proteins and peptides irrespective of sequence homology by support vector machines. PMID:20066123
Potential aggregation prone regions in biotherapeutics: A survey of commercial monoclonal antibodies. PMID:20065649
Computer-aided discovery, validation, and mechanistic characterization of novel neolignan activators of peroxisome proliferator-activated receptor gamma. PMID:20064974
Homologous over-extension: a challenge for iterative similarity searches. PMID:20064877
A pairwise residue contact area-based mean force potential for discrimination of native protein structure. PMID:20064218
Insights into the domain and repeat architecture of target of rapamycin. PMID:20060908
MolProbity: all-atom structure validation for macromolecular crystallography. PMID:20057044
SKPDB: a structural database of shikimate pathway enzymes. PMID:20055992
Prediction of structures of zinc-binding proteins through explicit modeling of metal coordination geometry. PMID:20054832
Binding of natural and synthetic polyphenols to human dihydrofolate reductase. PMID:20054477
Crystal structure of the Mp1p ligand binding domain 2 reveals its function as a fatty acid-binding protein. PMID:20053994
The effects of CapZ peptide (TRTK-12) binding to S100B-Ca2+ as examined by NMR and X-ray crystallography. PMID:20053360
Statistical method on nonrandom clustering with application to somatic mutations in cancer. PMID:20053295
PRTAD: a database for protein residue torsion angle distributions. PMID:20052908
Refinement of under-determined loops of Human Prion Protein by database-derived distance constraints. PMID:20052907
Linear-time protein 3-D structure searching with insertions and deletions. PMID:20047663
Involvement of the residues of GSKIP, AxinGID, and FRATtide in their binding with GSK3beta to unravel a novel C-terminal scaffold-binding region. PMID:20043192
Improving performance of docking-based virtual screening by structural filtration. PMID:20041273
The WD40 domain is required for LRRK2 neurotoxicity. PMID:20041156
The evolutionary history of protein domains viewed by species phylogeny. PMID:20041107
Comprehensive in silico prediction and analysis of chlamydial outer membrane proteins reflects evolution and life style of the Chlamydiae. PMID:20040079
Discriminating the native structure from decoys using scoring functions based on the residue packing in globular proteins. PMID:20038291
Evolutionary trace annotation of protein function in the structural proteome. PMID:20036248
Progress in elucidating the structural and dynamic character of G Protein-Coupled Receptor oligomers for use in drug discovery. PMID:20028319
A toolbox for ab initio 3-D reconstructions in single-particle electron microscopy. PMID:20018246
Determination of side-chain-rotamer and side-chain and backbone virtual-bond-stretching potentials of mean force from AM1 energy surfaces of terminally-blocked amino-acid residues, for coarse-grained simulations of protein structure and folding. II. Results, comparison with statistical potentials, and implementation in the UNRES force field. PMID:20017135
Prediction of protein-protein interaction sites using an ensemble method. PMID:20015386
Functional characterization of nonsynonymous single nucleotide polymorphisms in the human organic anion transporter 4 (hOAT4). PMID:20015291
Toward the discovery of vaccine adjuvants: coupling in silico screening and in vitro analysis of antagonist binding to human and mouse CCR4 receptors. PMID:20011659
Human cancer protein-protein interaction network: a structural perspective. PMID:20011507
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Modular prediction of protein structural classes from sequences of twilight-zone identity with predicting sequences. PMID:20003388
Recipes for the selection of experimental protein conformations for virtual screening. PMID:20000587
Mitochondrial dysfunction in mouse models of Parkinson's disease revealed by transcriptomics and proteomics. PMID:19967437
DNA-binding residues and binding mode prediction with binding-mechanism concerned models. PMID:19958487
The structure of the KlcA and ArdB proteins reveals a novel fold and antirestriction activity against Type I DNA restriction systems in vivo but not in vitro. PMID:20007596
Modular prediction of protein structural classes from sequences of twilight-zone identity with predicting sequences. PMID:20003388
Recipes for the selection of experimental protein conformations for virtual screening. PMID:20000587
Mitochondrial dysfunction in mouse models of Parkinson's disease revealed by transcriptomics and proteomics. PMID:19967437
DNA-binding residues and binding mode prediction with binding-mechanism concerned models. PMID:19958487
A sequence-based hybrid predictor for identifying conformationally ambivalent regions in proteins. PMID:19958486
A modular kernel approach for integrative analysis of protein domain boundaries. PMID:19958485
An electrostatic switch displaces phosphatidylinositol phosphate kinases from the membrane during phagocytosis. PMID:19951917
NMR characterization of membrane protein-detergent micelle solutions by use of microcoil equipment. PMID:19950959
Dynameomics: a consensus view of the protein unfolding/folding transition state ensemble across a diverse set of protein folds. PMID:19948125
A cytogenetic abnormality and rare coding variants identify ABCA13 as a candidate gene in schizophrenia, bipolar disorder, and depression. PMID:19944402
Docking of calcium ions in proteins with flexible side chains and deformable backbones. PMID:19937325
Pharmacophore-based virtual screening versus docking-based virtual screening: a benchmark comparison against eight targets. PMID:19935678
Transcription regulation of caspase-1 by R393 of HIPPI and its molecular partner HIP-1. PMID:19934260
SuperCYP: a comprehensive database on Cytochrome P450 enzymes including a tool for analysis of CYP-drug interactions. PMID:19934256
MUFOLD: A new solution for protein 3D structure prediction. PMID:19927325
Solution NMR structures of proteins VPA0419 from Vibrio parahaemolyticus and yiiS from Shigella flexneri provide structural coverage for protein domain family PFAM 04175. PMID:19927321
Catalytic water co-existing with a product peptide in the active site of HIV-1 protease revealed by X-ray structure analysis. PMID:19924250
A hydrogen-bonding network is important for oxidation and isomerization in the reaction catalyzed by cholesterol oxidase. PMID:19923719
Techniques and tactics used in determining the structure of the trimeric ebolavirus glycoprotein. PMID:19923712
Protein flexibility: coordinate uncertainties and interpretation of structural differences. PMID:19923711
GeMMA: functional subfamily classification within superfamilies of predicted protein structural domains. PMID:19923231
Sequence-structure relationships in RNA loops: establishing the basis for loop homology modeling. PMID:19923230
Comparing models of evolution for ordered and disordered proteins. PMID:19923193
Antidiabetic Bis-Maltolato-OxoVanadium(IV): conversion of inactive trans- to bioactive cis-BMOV for possible binding to target PTP-1B. PMID:19920909
ELM: the status of the 2010 eukaryotic linear motif resource. PMID:19920119
The relationship between water bridges and the polyproline II conformation: a large-scale analysis of molecular dynamics simulations and crystal structures. PMID:19917655
Binding hot spots and amantadine orientation in the influenza a virus M2 proton channel. PMID:19917240
DG-AMMOS: a new tool to generate 3d conformation of small molecules using distance geometry and automated molecular mechanics optimization for in silico screening. PMID:19912625
Thalidomide attenuates nitric oxide-driven angiogenesis by interacting with soluble guanylyl cyclase. PMID:19912234
A threading-based method for the prediction of DNA-binding proteins with application to the human genome. PMID:19911048
MeMotif: a database of linear motifs in alpha-helical transmembrane proteins. PMID:19910368
The cytochrome P450 engineering database: Integration of biochemical properties. PMID:19909539
Computational identification of slow conformational fluctuations in proteins. PMID:19908896
Loss of post-translational modification sites in disease. PMID:19908386
Phylogenetic analysis and homology modelling of Paracentrotus lividus nectin. PMID:19908157
Interactions between lipids and human anti-HIV antibody 4E10 can be reduced without ablating neutralizing activity. PMID:19906921
The UCSC Genome Browser database: update 2010. PMID:19906737
Protein Structure Initiative Material Repository: an open shared public resource of structural genomics plasmids for the biological community. PMID:19906724
3DNALandscapes: a database for exploring the conformational features of DNA. PMID:19906722
ComSin: database of protein structures in bound (complex) and unbound (single) states in relation to their intrinsic disorder. PMID:19906708
MicrobesOnline: an integrated portal for comparative and functional genomics. PMID:19906701
Toward a quantitative theory of intrinsically disordered proteins and their function. PMID:19903882
IMGT/3Dstructure-DB and IMGT/DomainGapAlign: a database and a tool for immunoglobulins or antibodies, T cell receptors, MHC, IgSF and MhcSF. PMID:19900967
Computational exploration of the network of sequence flow between protein structures. PMID:19899165
STITCH 2: an interaction network database for small molecules and proteins. PMID:19897548
Comparative virtual screening and novelty detection for NMDA-GlycineB antagonists. PMID:19890609
Collective dynamics of periplasmic glutamine binding protein upon domain closure. PMID:19883597
4-Pregnen-21-ol-3,20-dione-21-(4-bromobenzenesulfonate) (NSC 88915) and related novel steroid derivatives as tyrosyl-DNA phosphodiesterase (Tdp1) inhibitors. PMID:19883083
Homology modelling of a sensor histidine kinase from Aeromonas hydrophila. PMID:19882182
Identification and characterization of a novel deoxyhypusine synthase in Leishmania donovani. PMID:19880510
N-acylpolyamine inhibitors of HDM2 and HDMX binding to p53. PMID:19880322
Prediction of hot spot residues at protein-protein interfaces by combining machine learning and energy-based methods. PMID:19878545
4D prediction of protein (1)H chemical shifts. PMID:19876601
Mechanical strength of 17,134 model proteins and cysteine slipknots. PMID:19876372
Antibody-mediated synergy and interference in the neutralization of SARS-CoV at an epitope cluster on the spike protein. PMID:19861118
The crystal structure of the novobiocin biosynthetic enzyme NovP: the first representative structure for the TylF O-methyltransferase superfamily. PMID:19857499
The structural basis of pregnane X receptor binding promiscuity. PMID:19856963
A structure filter for the Eukaryotic Linear Motif Resource. PMID:19852836
Perturbation-response scanning reveals ligand entry-exit mechanisms of ferric binding protein. PMID:19851447
An atlas of the thioredoxin fold class reveals the complexity of function-enabling adaptations. PMID:19851441
A novel noncovalent complex of chorismate mutase and DAHP synthase from Mycobacterium tuberculosis: protein purification, crystallization and X-ray diffraction analysis. PMID:19851019
Crystallization and preliminary X-ray analysis of a D-Ala:D-Ser ligase associated with VanG-type vancomycin resistance. PMID:19851013
Evidence for the adaptation of protein pH-dependence to subcellular pH. PMID:19849832
A novel and efficient tool for locating and characterizing protein cavities and binding sites. PMID:19847777
Molecular docking screens using comparative models of proteins. PMID:19845314
A new method for publishing three-dimensional content. PMID:19841676
Crystal Structures of the histidine acid phosphatase from Francisella tularensis provide insight into substrate recognition. PMID:19836403
PeptideDepot: flexible relational database for visual analysis of quantitative proteomic data and integration of existing protein information. PMID:19834895
Insight into the interaction sites between fatty acid binding proteins and their ligands. PMID:19834748
Comprehensive classification of nucleotidyltransferase fold proteins: identification of novel families and their representatives in human. PMID:19833706
Extraction, integration and analysis of alternative splicing and protein structure distributed information. PMID:19828075
Conformational landscape of the human immunodeficiency virus type 1 reverse transcriptase non-nucleoside inhibitor binding pocket: lessons for inhibitor design from a cluster analysis of many crystal structures. PMID:19827836
Q-Dock(LHM): Low-resolution refinement for ligand comparative modeling. PMID:19827144
Design of high-affinity S100-target hybrid proteins. PMID:19827097
Finding molecular dioxygen tunnels in homoprotocatechuate 2,3-dioxygenase: implications for different reactivity of identical subunits. PMID:19826803
Identification of continuous human B-cell epitopes in the envelope glycoprotein of dengue virus type 3 (DENV-3). PMID:19826631
Equine rhinitis A virus and its low pH empty particle: clues towards an aphthovirus entry mechanism? PMID:19816570
The crystal structure of sphingosine-1-phosphate in complex with a Fab fragment reveals metal bridging of an antibody and its antigen. PMID:19815502
A stochastic context free grammar based framework for analysis of protein sequences. PMID:19814800
Searching for factors that distinguish disease-prone and disease-resistant prions via sequence analysis. PMID:19812771
Molecular models for intrastrand DNA G-quadruplexes. PMID:19811654
Knowledge-based characterization of similarity relationships in the human protein-tyrosine phosphatase family for rational inhibitor design. PMID:19810703
Quality Meshing of Implicit Solvation Models of Biomolecular Structures. PMID:19809581
Cancer and virus leads by HTS, chemical design and SEA data mining. PMID:19807668
Fast screening of protein surfaces using geometric invariant fingerprints. PMID:19805347
Quantum-mechanics-derived 13Calpha chemical shift server (CheShift) for protein structure validation. PMID:19805131
Nanosecond motions in proteins impose bounds on the timescale distributions of local dynamics. PMID:19804740
ProDaMa: an open source Python library to generate protein structure datasets. PMID:19799773
Quantitative prediction of protein-protein binding affinity with a potential of mean force considering volume correction. PMID:19798743
Betaalpha-hairpin clamps brace betaalphabeta modules and can make substantive contributions to the stability of TIM barrel proteins. PMID:19787060
LIBRUS: combined machine learning and homology information for sequence-based ligand-binding residue prediction. PMID:19786483
Highly sensitive detection of individual HEAT and ARM repeats with HHpred and COACH. PMID:19777061
High resolution NMR-based model for the structure of a scFv-IL-1beta complex: potential for NMR as a key tool in therapeutic antibody design and development. PMID:19776018
A new crystal form of human tear lipocalin reveals high flexibility in the loop region and induced fit in the ligand cavity. PMID:19770509
Modeling discrete heterogeneity in X-ray diffraction data by fitting multi-conformers. PMID:19770508
On the combination of molecular replacement and single-wavelength anomalous diffraction phasing for automated structure determination. PMID:19770506
A multivariate likelihood SIRAS function for phasing and model refinement. PMID:19770502
End-to-end and end-to-middle interhelical interactions: new classes of interacting helix pairs in protein structures. PMID:19770500
KING (Kinemage, Next Generation): a versatile interactive molecular and scientific visualization program. PMID:19768809
DECOMP: a PDB decomposition tool on the web. PMID:19759860
Analysis of protein chameleon sequence characteristics. PMID:19759809
An integrated approach to the interpretation of single amino acid polymorphisms within the framework of CATH and Gene3D. PMID:19758469
Extraction of human kinase mutations from literature, databases and genotyping studies. PMID:19758464
Interactions of the osmolyte glycine betaine with molecular surfaces in water: thermodynamics, structural interpretation, and prediction of m-values. PMID:19757837
Comparative sequence and structural analyses of G-protein-coupled receptor crystal structures and implications for molecular models. PMID:19756152
The Gene Wiki: community intelligence applied to human gene annotation. PMID:19755503
Understanding protein structure from a percolation perspective. PMID:19751685
Epitopia: a web-server for predicting B-cell epitopes. PMID:19751513
Design, synthesis, protein-ligand X-ray structure, and biological evaluation of a series of novel macrocyclic human immunodeficiency virus-1 protease inhibitors to combat drug resistance. PMID:19746963
Virtual Screening as a Technique for PPAR Modulator Discovery. PMID:19746174
Exploring kainate receptor pharmacology using molecular dynamics simulations. PMID:19737573
Importance of ligand reorganization free energy in protein-ligand binding-affinity prediction. PMID:19736924
The interaction of Bacillus subtilis sigmaA with RNA polymerase. PMID:19735077
Binding site of ABC transporter homology models confirmed by ABCB1 crystal structure. PMID:19732422
Shape and evolution of thermostable protein structure. PMID:19731381
Comparison of structure-based and threading-based approaches to protein functional annotation. PMID:19731377
Regression applied to protein binding site prediction and comparison with classification. PMID:19728868
The flexible pocketome engine for structural chemogenomics. PMID:19727619
Crystallization and preliminary X-ray diffraction studies of the ubiquitin-like (UbL) domain of the human homologue A of Rad23 (hHR23A) protein. PMID:19724136
Analysis of students' aptitude to provide meaning to images that represent cellular components at the molecular level. PMID:19723817
Identification, analysis, and prediction of protein ubiquitination sites. PMID:19722269
The major neutralizing antibody responses to recombinant anthrax lethal and edema factors are directed to non-cross-reactive epitopes. PMID:19720758
Pressure-dependent structure changes in barnase on ligand binding reveal intermediate rate fluctuations. PMID:19720037
An energetic representation of protein architecture that is independent of primary and secondary structure. PMID:19720035
Automated docking screens: a feasibility study. PMID:19719084
The human rhinovirus: human-pathological impact, mechanisms of antirhinoviral agents, and strategies for their discovery. PMID:19714577
Pushing structural information into the yeast interactome by high-throughput protein docking experiments. PMID:19714207
FLORA: a novel method to predict protein function from structure in diverse superfamilies. PMID:19714201
Computation of conformational coupling in allosteric proteins. PMID:19714199
Acetylsalicylic acid (aspirin) reduces damage to reconstituted human tissues infected with Candida species by inhibiting extracellular fungal lipases. PMID:19703582
Assessing the druggability of protein-protein interactions by a supervised machine-learning method. PMID:19703312
Toward the design of mutation-resistant enzyme inhibitors: further evaluation of the substrate envelope hypothesis. PMID:19703025
In silico structure-based design of a novel class of potent and selective small peptide inhibitor of Mycobacterium tuberculosis Dihydrofolate reductase, a potential target for anti-TB drug discovery. PMID:19697148
Computational design of Candida boidinii xylose reductase for altered cofactor specificity. PMID:19693930
A search for energy minimized sequences of proteins. PMID:19690619
Polarizable atomic multipole X-ray refinement: application to peptide crystals. PMID:19690373
Rotational order-disorder structure of fluorescent protein FP480. PMID:19690368
A comparative analysis of the equilibrium dynamics of a designed protein inferred from NMR, X-ray, and computations. PMID:19688820
Focused functional dynamics of supramolecules by use of a mixed-resolution elastic network model. PMID:19686666
REACH coarse-grained normal mode analysis of protein dimer interaction dynamics. PMID:19686664
Four distances between pairs of amino acids provide a precise description of their interaction. PMID:19680437
Multiscale generalized born modeling of ligand binding energies for virtual database screening. PMID:19678651
ArachnoServer: a database of protein toxins from spiders. PMID:19674480
Allergen databases: current status and perspectives. PMID:19671381
Modeling complex biological macromolecules: reduction of multibead models. PMID:19669537
Assessment of helical interfaces in protein-protein interactions. PMID:19668855
Knowledge-guided inference of domain-domain interactions from incomplete protein-protein interaction networks. PMID:19667081
Tertiary motifs revealed in analyses of higher-order RNA junctions. PMID:19660472
VENN, a tool for titrating sequence conservation onto protein structures. PMID:19656955
A proposed syntax for Minimotif Semantics, version 1. PMID:19656396
Influence of cation-pi interactions to the structural stability of prokaryotic and eukaryotic translation elongation factors. PMID:19653064
Simulation of structural and functional properties of mevalonate diphosphate decarboxylase (MVD). PMID:19653015
Complete amino-acid sequence, crystallization and preliminary X-ray diffraction studies of leucurolysin-a, a nonhaemorrhagic metalloproteinase from Bothrops leucurus snake venom. PMID:19652343
Metal-controlled interdomain cooperativity in parvalbumins. PMID:19651438
Automatic multiple-zone rigid-body refinement with a large convergence radius. PMID:19649324
A generic method for assignment of reliability scores applied to solvent accessibility predictions. PMID:19646261
Combining sequence and structural profiles for protein solvent accessibility prediction. PMID:19642280
A designed chimeric cyanovirin-N homolog lectin: structure and molecular basis of sucrose binding. PMID:19639634
The Tumbleweed: towards a synthetic proteinmotor. PMID:19639042
Structural models of human eEF1A1 and eEF1A2 reveal two distinct surface clusters of sequence variation and potential differences in phosphorylation. PMID:19636410
Web server suite for complex mixture analysis by covariance NMR. PMID:19634130
The first crystal structures of a family 19 class IV chitinase: the enzyme from Norway spruce. PMID:19629717
Enhancement of beta-sheet assembly by cooperative hydrogen bonds potential. PMID:19628506
Application of screening methods, shape signatures and engineered biosensors in early drug discovery process. PMID:19626425
Structural basis of the CD8 alpha beta/MHC class I interaction: focused recognition orients CD8 beta to a T cell proximal position. PMID:19625641
An in silico study of the molecular basis of B-RAF activation and conformational stability. PMID:19624854
Accuracy analysis of multiple structure alignments. PMID:19621383
Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS). PMID:19620974
Molecular determinants of snurportin 1 ligand affinity and structural response upon binding. PMID:19619473
Protein elastic network models and the ranges of cooperativity. PMID:19617554
Docking and 3D-QSAR studies on isatin sulfonamide analogues as caspase-3 inhibitors. PMID:19610597
Amino acid architecture that influences dNTP insertion efficiency in Y-family DNA polymerase V of E. coli. PMID:19607844
Analysis of loop boundaries using different local structure assignment methods. PMID:19606500
PSPP: a protein structure prediction pipeline for computing clusters. PMID:19606223
Improving structure-based function prediction using molecular dynamics. PMID:19604472
Target domain definition and classification in CASP8. PMID:19603487
A comprehensive analysis of the structure-function relationship in proteins based on local structure similarity. PMID:19603073
Conformational changes in redox pairs of protein structures. PMID:19598234
Toxoplasma gondii cathepsin L is the primary target of the invasion-inhibitory compound morpholinurea-leucyl-homophenyl-vinyl sulfone phenyl. PMID:19596863
Improvement of RNA secondary structure prediction using RNase H cleavage and randomized oligonucleotides. PMID:19596816
Sequence and structural analysis of the Asp-box motif and Asp-box beta-propellers; a widespread propeller-type characteristic of the Vps10 domain family and several glycoside hydrolase families. PMID:19594936
PDA: an automatic and comprehensive analysis program for protein-DNA complex structures. PMID:19594872
Prediction of DNA-binding residues from protein sequence information using random forests. PMID:19594868
Benefits of structural genomics for drug discovery research. PMID:19594422
Genomes2Drugs: identifies target proteins and lead drugs from proteome data. PMID:19593435
A conserved Na(+) binding site of the sodium-coupled neutral amino acid transporter 2 (SNAT2). PMID:19589777
Amyloidogenic determinants are usually not buried. PMID:19589171
Analyses on hydrophobicity and attractiveness of all-atom distance-dependent potentials. PMID:19588493
Structure of human Rad51 protein filament from molecular modeling and site-specific linear dichroism spectroscopy. PMID:19587234
Analysis of structured and intrinsically disordered regions of transmembrane proteins. PMID:19585006
Alpha-keto acid metabolites of naturally occurring organoselenium compounds as inhibitors of histone deacetylase in human prostate cancer cells. PMID:19584079
Model structure of APOBEC3C reveals a binding pocket modulating ribonucleic acid interaction required for encapsidation. PMID:19581596
In situ characterization of differences in the viscoelastic response of individual gram-negative and gram-positive bacterial cells. PMID:19581369
Drug discovery using chemical systems biology: repositioning the safe medicine Comtan to treat multi-drug and extensively drug resistant tuberculosis. PMID:19578428
Functional annotations for the Saccharomyces cerevisiae genome: the knowns and the known unknowns. PMID:19577472
Ensemble approach to predict specificity determinants: benchmarking and validation. PMID:19573245
Assessing the accuracy of protein structures by quantum mechanical computations of 13C(alpha) chemical shifts. PMID:19572703
An N log N approximation based on the natural organization of biomolecules for speeding up the computation of long range interactions. PMID:19569183
Relative stabilities of conserved and non-conserved structures in the OB-fold superfamily. PMID:19564956
Functional annotations for the Saccharomyces cerevisiae genome: the knowns and the known unknowns. PMID:19577472
Ensemble approach to predict specificity determinants: benchmarking and validation. PMID:19573245
Assessing the accuracy of protein structures by quantum mechanical computations of 13C(alpha) chemical shifts. PMID:19572703
An N log N approximation based on the natural organization of biomolecules for speeding up the computation of long range interactions. PMID:19569183
Relative stabilities of conserved and non-conserved structures in the OB-fold superfamily. PMID:19564956
Interpretation of very low resolution X-ray electron-density maps using core objects. PMID:19564689
ResBoost: characterizing and predicting catalytic residues in enzymes. PMID:19558703
Ab initio and homology based prediction of protein domains by recursive neural networks. PMID:19558651
Determination and application of empirically derived detergent phase boundaries to effectively crystallize membrane proteins. PMID:19554626
Blind docking of pharmaceutically relevant compounds using RosettaLigand. PMID:19554568
Web application for studying the free energy of binding and protonation states of protein-ligand complexes based on HINT. PMID:19554265
The phox domain of sorting nexin 5 lacks phosphatidylinositol 3-phosphate (PtdIns(3)P) specificity and preferentially binds to phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2). PMID:19553671
Global distribution of conformational states derived from redundant models in the PDB points to non-uniqueness of the protein structure. PMID:19553204
Correlation of RNA secondary structure statistics with thermodynamic stability and applications to folding. PMID:19540243
Massive non-natural proteins structure prediction using grid technologies. PMID:19534748
A chemogenomics view on protein-ligand spaces. PMID:19534738
PSI-2: structural genomics to cover protein domain family space. PMID:19523904
Homology modeling of human Toll-like receptors TLR7, 8, and 9 ligand-binding domains. PMID:19521997
On the origins of enzyme inhibitor selectivity and promiscuity: a case study of protein kinase binding to staurosporine. PMID:19519740
In silico studies on DARC. PMID:19519483
Molecular dynamics simulation study of the binding of purine bases to the aptamer domain of the guanine sensing riboswitch. PMID:19515936
N-terminal strands of filamin Ig domains act as a conformational switch under biological forces. PMID:19514078
Characterization of the wheat endosperm transfer cell-specific protein TaPR60. PMID:19513805
A dyad of lymphoblastic lysosomal cysteine proteases degrades the antileukemic drug L-asparaginase. PMID:19509471
Thermodynamic characterization of tandem mismatches found in naturally occurring RNA. PMID:19509311
Integrating statistical predictions and experimental verifications for enhancing protein-chemical interaction predictions in virtual screening. PMID:19503826
Evolutionary pressure on mitochondrial cytochrome b is consistent with a role of CytbI7T affecting longevity during caloric restriction. PMID:19503808
FINDSITE: a threading-based approach to ligand homology modeling. PMID:19503616
Using genome-wide measurements for computational prediction of SH2-peptide interactions. PMID:19502496
Cavities in protein-DNA and protein-RNA interfaces. PMID:19494181
Molecular distinctions between Aurora A and B: a single residue change transforms Aurora A into correctly localized and functional Aurora B. PMID:19494039
Modelling substrate specificity and enantioselectivity for lipases and esterases by substrate-imprinted docking. PMID:19493341
Protein intrinsic disorder and influenza virulence: the 1918 H1N1 and H5N1 viruses. PMID:19493338
A sequence and structure based method to predict putative substrates, functions and regulatory networks of endo proteases. PMID:19492082
Vibrational dynamics of icosahedrally symmetric biomolecular assemblies compared with predictions based on continuum elasticity. PMID:19486668
Reconstruction and stability of secondary structure elements in the context of protein structure prediction. PMID:19486664
Probing ligand binding modes of Mycobacterium tuberculosis MurC ligase by molecular modeling, dynamics simulation and docking. PMID:19484275
ProteDNA: a sequence-based predictor of sequence-specific DNA-binding residues in transcription factors. PMID:19483101
Structural and functional analysis of Campylobacter jejuni PseG: a udp-sugar hydrolase from the pseudaminic acid biosynthetic pathway. PMID:19483088
Discrete-continuous duality of protein structure space. PMID:19482467
Covalent cross-linking of glutathione and carnosine to proteins by 4-oxo-2-nonenal. PMID:19480392
Empirical estimation of the energetic contribution of individual interface residues in structures of protein-protein complexes. PMID:19479323
A unified statistical model to support local sequence order independent similarity searching for ligand-binding sites and its application to genome-based drug discovery. PMID:19478004
Prediction of sub-cavity binding preferences using an adaptive physicochemical structure representation. PMID:19478002
Pokefind: a novel topological filter for use with protein structure prediction. PMID:19478000
Inhibition of ATP synthase by chlorinated adenosine analogue. PMID:19477165
Biases in Drosophila melanogaster protein trap screens. PMID:19476619
Web 3DNA--a web server for the analysis, reconstruction, and visualization of three-dimensional nucleic-acid structures. PMID:19474339
Design of HIV-1 protease inhibitors with pyrrolidinones and oxazolidinones as novel P1'-ligands to enhance backbone-binding interactions with protease: synthesis, biological evaluation, and protein-ligand X-ray studies. PMID:19473017
Motif-directed flexible backbone design of functional interactions. PMID:19472357
Computational structural analysis of an anti-L-amino acid antibody and inversion of its stereoselectivity. PMID:19472280
Kinetoplastid RNA editing ligases 1 and 2 exhibit different electrostatic properties. PMID:19471975
Buffer optimization of thermal melt assays of Plasmodium proteins for detection of small-molecule ligands. PMID:19470714
Small molecules bound to unique sites in the target protein binding cleft of calcium-bound S100B as characterized by nuclear magnetic resonance and X-ray crystallography. PMID:19469484
Insight into ligand selectivity in HCV NS5B polymerase: molecular dynamics simulations, free energy decomposition and docking. PMID:19466613
Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard. PMID:19465773
HotSpot Wizard: a web server for identification of hot spots in protein engineering. PMID:19465397
COPS--a novel workbench for explorations in fold space. PMID:19465386
The SALAMI protein structure search server. PMID:19465380
RHYTHM--a server to predict the orientation of transmembrane helices in channels and membrane-coils. PMID:19465378
SEPPA: a computational server for spatial epitope prediction of protein antigens. PMID:19465377
Increasingly accurate dynamic molecular models of G-protein coupled receptor oligomers: Panacea or Pandora's box for novel drug discovery? PMID:19465029
Defective interaction between Pol2p and Dpb2p, subunits of DNA polymerase epsilon, contributes to a mutator phenotype in Saccharomyces cerevisiae. PMID:19463834
Databases and QSAR for cancer research. PMID:19458762
Bioinformatics resources for cancer research with an emphasis on gene function and structure prediction tools. PMID:19458756
RosettaAntibody: antibody variable region homology modeling server. PMID:19458157
Detection of the TCDD binding-fingerprint within the Ah receptor ligand binding domain by structurally driven mutagenesis and functional analysis. PMID:19456125
Multiple property tolerance analysis for the evaluation of missense mutations. PMID:19455225
Universal partitioning of the hierarchical fold network of 50-residue segments in proteins. PMID:19454039
Tableau-based protein substructure search using quadratic programming. PMID:19450287
Analysis of four-way junctions in RNA structures. PMID:19445952
@TOME-2: a new pipeline for comparative modeling of protein-ligand complexes. PMID:19443448
MM-align: a quick algorithm for aligning multiple-chain protein complex structures using iterative dynamic programming. PMID:19443443
Use of molecular modeling, docking, and 3D-QSAR studies for the determination of the binding mode of benzofuran-3-yl-(indol-3-yl)maleimides as GSK-3beta inhibitors. PMID:19440740
Prediction of mono- and di-nucleotide-specific DNA-binding sites in proteins using neural networks. PMID:19439068
The structural basis for the difference in absorbance spectra for the FMO antenna protein from various green sulfur bacteria. PMID:19437128
Drug discovery using chemical systems biology: identification of the protein-ligand binding network to explain the side effects of CETP inhibitors. PMID:19436720
COMPASS server for homology detection: improved statistical accuracy, speed and functionality. PMID:19435884
FASTR3D: a fast and accurate search tool for similar RNA 3D structures. PMID:19435878
Web services at the European Bioinformatics Institute-2009. PMID:19435877
Conformational variability of benzamidinium-based inhibitors. PMID:19435349
Consistent improvement of cross-docking results using binding site ensembles generated with elastic network normal modes. PMID:19434904
SLITHER: a web server for generating contiguous conformations of substrate molecules entering into deep active sites of proteins or migrating through channels in membrane transporters. PMID:19433508
Conserved water-mediated H-bonding dynamics of catalytic Asn 175 in plant thiol protease. PMID:19430116
SuperLooper--a prediction server for the modeling of loops in globular and membrane proteins. PMID:19429894
HHomp--prediction and classification of outer membrane proteins. PMID:19429691
The crystal structures of substrate and nucleotide complexes of Enterococcus faecium aminoglycoside-2''-phosphotransferase-IIa [APH(2'')-IIa] provide insights into substrate selectivity in the APH(2'') subfamily. PMID:19429619
Mixture of experts models to exploit global sequence similarity on biomolecular sequence labeling. PMID:19426452
Efficient use of unlabeled data for protein sequence classification: a comparative study. PMID:19426450
AUTOMATIC STRUCTURE INTERPRETATION OF SINGLE PARTICLE CRYO-ELECTRON MICROSCOPY: FROM IMAGES TO PSUEDO-ATOMIC MODELS. PMID:19424455
X-ray vs. NMR structures as templates for computational protein design. PMID:19422060
Vaccinia virus G8R protein: a structural ortholog of proliferating cell nuclear antigen (PCNA). PMID:19421403
iSARST: an integrated SARST web server for rapid protein structural similarity searches. PMID:19420060
Protinfo PPC: a web server for atomic level prediction of protein complexes. PMID:19420059
Solution structure of factor I-like modules from complement C7 reveals a pair of follistatin domains in compact pseudosymmetric arrangement. PMID:19419965
Improving consensus contact prediction via server correlation reduction. PMID:19419562
RASMOT-3D PRO: a 3D motif search webserver. PMID:19417073
Substrate specificity of streptococcal unsaturated glucuronyl hydrolases for sulfated glycosaminoglycan. PMID:19416976
Improving classification in protein structure databases using text mining. PMID:19416501
Identifying the structure of the active sites of human recombinant prolidase. PMID:19415262
Urea impedes the hydrophobic collapse of partially unfolded proteins. PMID:19413980
Prediction of protein binding regions in disordered proteins. PMID:19412530
WISDOM-II: screening against multiple targets implicated in malaria using computational grid infrastructures. PMID:19409081
Owner controlled data exchange in nutrigenomic collaborations: the NuGO information network. PMID:19408032
Structure of pig heart citrate synthase at 1.78 A resolution. PMID:19407370
Absolute FKBP binding affinities obtained via nonequilibrium unbinding simulations. PMID:19405629
Structural analysis of trypanosomal sirtuin: an insight for selective drug design. PMID:19404761
Molecular and biochemical characterization of the parvulin-type PPIases in Lotus japonicus. PMID:19403733
In vivo tumor targeting and imaging with engineered trivalent antibody fragments containing collagen-derived sequences. PMID:19401768
Conservation and variability of West Nile virus proteins. PMID:19401763
Nothing about protein structure classification makes sense except in the light of evolution. PMID:19394812
Small local variations in B-form DNA lead to a large variety of global geometries which can accommodate most DNA-binding protein motifs. PMID:19393049
Assessment of the optimization of affinity and specificity at protein-DNA interfaces. PMID:19389725
Dictyostelium discoideum--a model for many reasons. PMID:19387798
Identifying native-like protein structures with scoring functions based on all-atom ECEPP force fields, implicit solvent models and structure relaxation. PMID:19384995
Assigning membrane binding geometry of cytochrome C by polarized light spectroscopy. PMID:19383483
All-atom contact model for understanding protein dynamics from crystallographic B-factors. PMID:19383453
Automated site preparation in physics-based rescoring of receptor ligand complexes. PMID:19382204
Allosteric transitions of supramolecular systems explored by network models: application to chaperonin GroEL. PMID:19381265
Detection of discriminative sequence patterns in the neighborhood of proline cis peptide bonds and their functional annotation. PMID:19379512
Computational methods for predicting sites of functionally important dynamics. PMID:19378962
Systematic comparison of SCOP and CATH: a new gold standard for protein structure analysis. PMID:19374763
DOCK 6: combining techniques to model RNA-small molecule complexes. PMID:19369428
Origin of slow relaxation following photoexcitation of W7 in myoglobin and the dynamics of its hydration layer. PMID:19368022
Increased hydrophobicity at the N terminus/membrane interface impairs gating of the severe combined immunodeficiency-related ORAI1 mutant. PMID:19366689
Crystal structure of Bacillus anthracis dihydrofolate reductase with the dihydrophthalazine-based trimethoprim derivative RAB1 provides a structural explanation of potency and selectivity. PMID:19364848
Visualizing sequence-governed nucleotide selectivities and mutagenic consequences through a replicative cycle: processing of a bulky carcinogen N2-dG lesion in a Y-family DNA polymerase. PMID:19364137
Configurational entropy in protein-peptide binding: computational study of Tsg101 ubiquitin E2 variant domain with an HIV-derived PTAP nonapeptide. PMID:19362095
An estimate of the numbers and density of low-energy structures (or decoys) in the conformational landscape of proteins. PMID:19357778
dndDB: a database focused on phosphorothioation of the DNA backbone. PMID:19357771
ModLink+: improving fold recognition by using protein-protein interactions. PMID:19357100
ProtSA: a web application for calculating sequence specific protein solvent accessibilities in the unfolded ensemble. PMID:19356231
Accessibility and partner number of protein residues, their relationship and a webserver, ContPlot for their display. PMID:19356223
Allosteric modulation of SULT2A1 by celecoxib and nimesulide: computational analyses. PMID:19356094
A database of domain definitions for proteins with complex interdomain geometry. PMID:19352501
Homology modelling: a review about the method on hand of the diabetic antigen GAD 65 structure prediction. PMID:19343288
An ivermectin-sensitive glutamate-gated chloride channel from the parasitic nematode Haemonchus contortus. PMID:19336526
Cyndi: a multi-objective evolution algorithm based method for bioactive molecular conformational generation. PMID:19335906
Insights into the high fidelity of a DNA polymerase I mutant. PMID:19333629
ProteinShader: illustrative rendering of macromolecules. PMID:19331660
Group B streptococcus pullulanase crystal structures in the context of a novel strategy for vaccine development. PMID:19329633
Protein structure prediction: when is it useful? PMID:19327982
Building and assessing atomic models of proteins from structural templates: learning and benchmarks. PMID:19326457
BETASCAN: probable beta-amyloids identified by pairwise probabilistic analysis. PMID:19325876
Accurate prediction of peptide binding sites on protein surfaces. PMID:19325869
Computational study for protein-protein docking using global optimization and empirical potentials. PMID:19325720
FINDSITE: a combined evolution/structure-based approach to protein function prediction. PMID:19324930
Compensatory mutations are repeatable and clustered within proteins. PMID:19324785
Hydrodynamic multibead modeling: problems, pitfalls, and solutions. 2. Proteins. PMID:19308400
Evolutionary Trace Annotation Server: automated enzyme function prediction in protein structures using 3D templates. PMID:19307237
Periodic sequence distribution of product ion abundances in electron capture dissociation of amphipathic peptides and proteins. PMID:19297190
The PHA Depolymerase Engineering Database: A systematic analysis tool for the diverse family of polyhydroxyalkanoate (PHA) depolymerases. PMID:19296857
Molecular determinants archetypical to the phylum Nematoda. PMID:19296854
The Open AUC Project. PMID:19296095
Docking study of triphenylphosphonium cations as estrogen receptor alpha modulators. PMID:19293997
Molecular basis for Bcl-2 homology 3 domain recognition in the Bcl-2 protein family: identification of conserved hot spot interactions. PMID:19293158
A coarse-grained potential for fold recognition and molecular dynamics simulations of proteins. PMID:19291741
Structure of the 12-subunit RNA polymerase II refined with the aid of anomalous diffraction data. PMID:19289466
A reexamination of correlations of amino acids with particular secondary structures. PMID:19280326
Hydrodynamic multibead modeling: problems, pitfalls, and solutions. 1. Ellipsoid models. PMID:19280183
A recurrent magnesium-binding motif provides a framework for the ribosomal peptidyl transferase center. PMID:19279186
Path-integral method for predicting relative binding affinities of protein-ligand complexes. PMID:19275144
Identification of coevolving residues and coevolution potentials emphasizing structure, bond formation and catalytic coordination in protein evolution. PMID:19274093
A feature-based approach to modeling protein-protein interaction hot spots. PMID:19273533
Structural conservation of a short, functional, peptide-sequence motif. PMID:19273121
Protein dynamics of a beta-sheet protein. PMID:19271215
Synthesis of casimiroin and optimization of its quinone reductase 2 and aromatase inhibitory activities. PMID:19265439
Modeling kinetics of subcellular disposition of chemicals. PMID:19265398
Functional group based Ligand binding affinity scoring function at atomic environmental level. PMID:19255647
New tips for structure prediction by comparative modeling. PMID:19255646
Functional insights by comparison of modeled structures of 18kDa small heat shock protein and its mutant in Mycobacterium leprae. PMID:19255639
Pre-docking filter for protein and ligand 3D structures. PMID:19255632
A preliminary neutron diffraction study of gamma-chymotrypsin. PMID:19255494
High-resolution structure of proteinase K cocrystallized with digalacturonic acid. PMID:19255463
A combination of hand-held models and computer imaging programs helps students answer oral questions about molecular structure and function: a controlled investigation of student learning. PMID:19255134
Thermostability of the N-terminal RNA-binding domain of the SARS-CoV nucleocapsid protein: experiments and numerical simulations. PMID:19254548
Rapid sampling of molecular motions with prior information constraints. PMID:19247429
Protein structure prediction on the Web: a case study using the Phyre server. PMID:19247286
Signatures of protein-DNA recognition in free DNA binding sites. PMID:19244617
Predicting helix-helix interactions from residue contacts in membrane proteins. PMID:19244388
Protein-protein interaction as a predictor of subcellular location. PMID:19243629
Structure and function of Pseudomonas aeruginosa protein PA1324 (21-170). PMID:19241370
A beginner's guide to radiation damage. PMID:19240325
A survey of available tools and web servers for analysis of protein-protein interactions and interfaces. PMID:19240123
BEID: database for sequence-structure-function information on antigen-antibody interactions. PMID:19238231
Ranking of binding and nonbinding peptides to MHC class I molecules using inverse folding approach: implications for vaccine design. PMID:19238199
Crystallographic model quality at a glance. PMID:19237753
iMembrane: homology-based membrane-insertion of proteins. PMID:19237449
The implementation of SOMO (SOlution MOdeller) in the UltraScan analytical ultracentrifugation data analysis suite: enhanced capabilities allow the reliable hydrodynamic modeling of virtually any kind of biomacromolecule. PMID:19234696
ABC transporters: the power to change. PMID:19234479
Identification of DNA-binding proteins using structural, electrostatic and evolutionary features. PMID:19233205
Inferential optimization for simultaneous fitting of multiple components into a CryoEM map of their assembly. PMID:19233204
Structural and electrostatic characterization of pariacoto virus: implications for viral assembly. PMID:19226622
Protein function annotation by homology-based inference. PMID:19226439
2-(3,4-dihydro-4-oxothieno[2,3-d]pyrimidin-2-ylthio) acetamides as a new class of falcipain-2 inhibitors. 3. design, synthesis and biological evaluation. PMID:19223827
KinImmerse: Macromolecular VR for NMR ensembles. PMID:19222844
Phylogenetic analysis and molecular evolution of guanine deaminases: from guanine to dendrites. PMID:19221682
Investigation of atomic level patterns in protein--small ligand interactions. PMID:19221587
HistoneHits: a database for histone mutations and their phenotypes. PMID:19218532
Homology modeling and site-directed mutagenesis reveal catalytic key amino acids of 3beta-hydroxysteroid-dehydrogenase/C4-decarboxylase from Arabidopsis. PMID:19218365
Correlated motions and interactions at the onset of the DNA-induced partial unfolding of Ets-1. PMID:19217849
Ions and inhibitors in the binding site of HIV protease: comparison of Monte Carlo simulations and the linearized Poisson-Boltzmann theory. PMID:19217848
Computational study of the heterodimerization between mu and delta receptors. PMID:19214754
Conservation of helical bundle structure between the exocyst subunits. PMID:19214222
Allergen Atlas: a comprehensive knowledge center and analysis resource for allergen information. PMID:19213741
Phylogenomics of DNA topoisomerases: their origin and putative roles in the emergence of modern organisms. PMID:19208647
Characterization of the structural features and interactions of sclerostin: molecular insight into a key regulator of Wnt-mediated bone formation. PMID:19208630
TransCent: computational enzyme design by transferring active sites and considering constraints relevant for catalysis. PMID:19208235
Studying the unfolding process of protein G and protein L under physical property space. PMID:19208146
SE: an algorithm for deriving sequence alignment from a pair of superimposed structures. PMID:19208141
Multi-constraint computational design suggests that native sequences of germline antibody H3 loops are nearly optimal for conformational flexibility. PMID:19194863
Prediction of interacting protein pairs from sequence using a Bayesian method. PMID:19194789
A critical cross-validation of high throughput structural binding prediction methods for pMHC. PMID:19194661
Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of the small subunit of isopropylmalate isomerase (Rv2987c) from Mycobacterium tuberculosis. PMID:19194004
Structural determinants responsible for substrate recognition and mode of action in family 11 polysaccharide lyases. PMID:19193638
Y-Family DNA polymerases may use two different dNTP shapes for insertion: a hypothesis and its implications. PMID:19188081
Structural analysis reveals DNA binding properties of Rv2827c, a hypothetical protein from Mycobacterium tuberculosis. PMID:19184528
Cold adaptation of zinc metalloproteases in the thermolysin family from deep sea and arctic sea ice bacteria revealed by catalytic and structural properties and molecular dynamics: new insights into relationship between conformational flexibility and hydrogen bonding. PMID:19181663
StoneHinge: hinge prediction by network analysis of individual protein structures. PMID:19180449
Vulnerability in Popular Molecular Dynamics Packages Concerning Langevin and Andersen Dynamics. PMID:19180249
Prediction of protein-protein interaction sites in sequences and 3D structures by random forests. PMID:19180183
DAP-kinase-mediated phosphorylation on the BH3 domain of beclin 1 promotes dissociation of beclin 1 from Bcl-XL and induction of autophagy. PMID:19180116
RosettaHoles: rapid assessment of protein core packing for structure prediction, refinement, design, and validation. PMID:19177366
Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques. PMID:19176554
Prediction of protein-protein interaction types using association rule based classification. PMID:19173748
Structural and dynamic effects of cholesterol at preferred sites of interaction with rhodopsin identified from microsecond length molecular dynamics simulations. PMID:19173312
An unusually small dimer interface is observed in all available crystal structures of cytosolic sulfotransferases. PMID:19173308
Analysis of errors in the structure determination of MsbA. PMID:19171975
Re-refinement from deposited X-ray data can deliver improved models for most PDB entries. PMID:19171973
Analysis and validation of carbohydrate three-dimensional structures. PMID:19171971
On vital aid: the why, what and how of validation. PMID:19171968
Model-building strategies for low-resolution X-ray crystallographic data. PMID:19171966
Residual structure within the disordered C-terminal segment of p21(Waf1/Cip1/Sdi1) and its implications for molecular recognition. PMID:19165719
Protein acrobatics in pairs--dimerization via domain swapping. PMID:19162470
Using least median of squares for structural superposition of flexible proteins. PMID:19159484
2-amido-3-(1H-indol-3-yl)-N-substituted-propanamides as a new class of falcipain-2 inhibitors. 1. Design, synthesis, biological evaluation and binding model studies. PMID:19158658
Identification of novel DNA repair proteins via primary sequence, secondary structure, and homology. PMID:19154573
Scoring confidence index: statistical evaluation of ligand binding mode predictions. PMID:19153808
Crystallization and preliminary crystallographic analysis of cgHle, a homoserine acetyltransferase homologue, from Corynebacterium glutamicum. PMID:19153452
The structure of d(CACACG).d(CGTGTG). PMID:19153446
Conformational dynamics of the flexible catalytic loop in Mycobacterium tuberculosis 1-deoxy-D-xylulose 5-phosphate reductoisomerase. PMID:19152632
Heme uptake across the outer membrane as revealed by crystal structures of the receptor-hemophore complex. PMID:19144921
Second messenger-mediated spatiotemporal control of protein degradation regulates bacterial cell cycle progression. PMID:19136627
Structural alphabets for protein structure classification: a comparison study. PMID:19135454
Movements of native C505 during channel gating in CNGA1 channels. PMID:19132361
RNA structure prediction from evolutionary patterns of nucleotide composition. PMID:19129237
Large-scale prediction of long disordered regions in proteins using random forests. PMID:19128505
Mesothelin, Stereocilin, and Otoancorin are predicted to have superhelical structures with ARM-type repeats. PMID:19128473
Comparisons of experimental and computed protein anisotropic temperature factors. PMID:19127591
A generalized knowledge-based discriminatory function for biomolecular interactions. PMID:19127590
Questioning the ubiquity of neofunctionalization. PMID:19119408
Molecular dynamics study of the interaction between fatty acid binding proteins with palmitate mini-micelles. PMID:19118410
Pyrrolysyl-tRNA synthetase-tRNA(Pyl) structure reveals the molecular basis of orthogonality. PMID:19118381
Analysis on conservation of disulphide bonds and their structural features in homologous protein domain families. PMID:19111067
Probing hemoglobin structure by means of traveling-wave ion mobility mass spectrometry. PMID:19110442
The meaning of alignment: lessons from structural diversity. PMID:19105835
Prediction of protein-protein binding site by using core interface residue and support vector machine. PMID:19102736
PocketMatch: a new algorithm to compare binding sites in protein structures. PMID:19091072
Flanking signal and mature peptide residues influence signal peptide cleavage. PMID:19091014
Molecular docking studies of dithionitrobenzoic acid and its related compounds to protein disulfide isomerase: computational screening of inhibitors to HIV-1 entry. PMID:19091013
Four-dimensional docking: a fast and accurate account of discrete receptor flexibility in ligand docking. PMID:19090659
Evolutionary and structural analyses of alpha-papillomavirus capsid proteins yields novel insights into L2 structure and interaction with L1. PMID:19087355
Analysis of mammalian gene batteries reveals both stable ancestral cores and highly dynamic regulatory sequences. PMID:19087242
Vicinity analysis: a methodology for the identification of similar protein active sites. PMID:19085023
The UniProtKB/Swiss-Prot knowledgebase and its Plant Proteome Annotation Program. PMID:19084081
Data deposition and annotation at the worldwide protein data bank. PMID:19082769
The Role of the Tight-Turn, Broken Hydrogen Bonding, Glu222 and Arg96 in the Post-translational Green Fluorescent Protein Chromophore Formation. PMID:19079566
Knottin cyclization: impact on structure and dynamics. PMID:19077275
Accommodation of an N-(deoxyguanosin-8-yl)-2-acetylaminofluorene adduct in the active site of human DNA polymerase iota: Hoogsteen or Watson-Crick base pairing? PMID:19072536
Photophysics and dihedral freedom of the chromophore in yellow, blue, and green fluorescent protein. PMID:19067572
EGF domain II of protein Pb28 from Plasmodium berghei interacts with monoclonal transmission blocking antibody 13.1. PMID:19066995
Residue contact-count potentials are as effective as residue-residue contact-type potentials for ranking protein decoys. PMID:19063740
Identification of xenoestrogens in food additives by an integrated in silico and in vitro approach. PMID:19063592
Toward high-resolution homology modeling of antibody Fv regions and application to antibody-antigen docking. PMID:19062174
Selecting optimum eukaryotic integral membrane proteins for structure determination by rapid expression and solubilization screening. PMID:19061901
A very large C-loop in EGF domain IV is characteristic of the P28 family of ookinete surface proteins. PMID:19057932
Improving accuracy of multiple sequence alignment algorithms based on alignment of neighboring residues. PMID:19056820
Module evolution and substrate specificity of fungal nonribosomal peptide synthetases involved in siderophore biosynthesis. PMID:19055762
SELECTpro: effective protein model selection using a structure-based energy function resistant to BLUNDERs. PMID:19055744
ElliPro: a new structure-based tool for the prediction of antibody epitopes. PMID:19055730
Type-II kinase inhibitor docking, screening, and profiling using modified structures of active kinase states. PMID:19053777
Spatial autocorrelation of amino Acid replacement rates in the vasopressin receptor family. PMID:19052795
Exploring the binding of HIV-1 integrase inhibitors by comparative residue interaction analysis (CoRIA). PMID:19048312
A disulfide linked model of the complement protein C8gamma complexed with C8alpha indel peptide. PMID:19048311
Search for inhibitors of aminoacyl-tRNA synthases by virtual click chemistry. PMID:19048310
Structural studies of shikimate dehydrogenase from Bacillus anthracis complexed with cofactor NADP. PMID:19043750
Modeling of Escherichia coli Endonuclease V structure in complex with DNA. PMID:19043748
Classifying Variants of Undetermined Significance in BRCA2 with protein likelihood ratios. PMID:19043619
Arena3D: visualization of biological networks in 3D. PMID:19040715
Protein chaperones Q8ZP25_SALTY from Salmonella typhimurium and HYAE_ECOLI from Escherichia coli exhibit thioredoxin-like structures despite lack of canonical thioredoxin active site sequence motif. PMID:19039680
Identification of structurally conserved residues of proteins in absence of structural homologs using neural network ensemble. PMID:19038986
SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny. PMID:19036790
Structural descriptor database: a new tool for sequence-based functional site prediction. PMID:19032768
The ribosome structure controls and directs mRNA entry, translocation and exit dynamics. PMID:19029596
Identification of channel-lining amino acid residues in the hydrophobic segment of colicin Ia. PMID:19029376
PDBalert: automatic, recurrent remote homology tracking and protein structure prediction. PMID:19025670
Mutations on the Switch III region and the alpha3 helix of Galpha16 differentially affect receptor coupling and regulation of downstream effectors. PMID:19025606
An interrupted beta-propeller and protein disorder: structural bioinformatics insights into the N-terminus of alsin. PMID:19023603
Formation of stable homodimer via the C-terminal alpha-helical domain of coronavirus nonstructural protein 9 is critical for its function in viral replication. PMID:19022466
Electron spin resonance shows common structural features for different classes of EcoRI-DNA complexes. PMID:19021169
Fibronectin unfolding revisited: modeling cell traction-mediated unfolding of the tenth type-III repeat. PMID:19020673
Proteomics studies confirm the presence of alternative protein isoforms on a large scale. PMID:19017398
Influenza sequence and epitope database. PMID:19015128
AS-ALPS: a database for analyzing the effects of alternative splicing on protein structure, interaction and network in human and mouse. PMID:19015123
The protein structure initiative structural genomics knowledgebase. PMID:19010965
Polar or apolar--the role of polarity for urea-induced protein denaturation. PMID:19008937
Prediction of DNA-binding residues in proteins from amino acid sequences using a random forest model with a hybrid feature. PMID:19008251
Predicting DNA recognition by Cys2His2 zinc finger proteins. PMID:19008249
Cavities and atomic packing in protein structures and interfaces. PMID:19005575
SuperToxic: a comprehensive database of toxic compounds. PMID:19004875
Collective dynamics of the ribosomal tunnel revealed by elastic network modeling. PMID:19004020
Analysis of the electrochemistry of hemes with E(m)s spanning 800 mV. PMID:19003997
Autofix for backward-fit sidechains: using MolProbity and real-space refinement to put misfits in their place. PMID:19002604
Predicting the energetics of conformational fluctuations in proteins from sequence: a strategy for profiling the proteome. PMID:19000815
PDBsum new things. PMID:18996896
Evolutionary modeling of rate shifts reveals specificity determinants in HIV-1 subtypes. PMID:18989394
MoKCa database--mutations of kinases in cancer. PMID:18986996
LRRML: a conformational database and an XML description of leucine-rich repeats (LRRs). PMID:18986514
Improved scoring function for comparative modeling using the M4T method. PMID:18985440
Evaluation of methods to cap molecular fragments in calculating energies of interaction in avian pancreatic polypeptide. PMID:18985167
The Role of Aromatic Residues in Stabilizing the Secondary and Tertiary Structure of Avian Pancreatic Polypeptide. PMID:18985166
ExDom: an integrated database for comparative analysis of the exon-intron structures of protein domains in eukaryotes. PMID:18984624
Relevance of biallelic versus monoallelic TNFRSF13B mutations in distinguishing disease-causing from risk-increasing TNFRSF13B variants in antibody deficiency syndromes. PMID:18981294
Sequential B-cell epitopes of Bacillus anthracis lethal factor bind lethal toxin-neutralizing antibodies. PMID:18981257
VIPERdb2: an enhanced and web API enabled relational database for structural virology. PMID:18981051
FitEM2EM--tools for low resolution study of macromolecular assembly and dynamics. PMID:18974836
The rough guide to in silico function prediction, or how to use sequence and structure information to predict protein function. PMID:18974821
Substitution of aminomethyl at the meta-position enhances the inactivation of O6-alkylguanine-DNA alkyltransferase by O6-benzylguanine. PMID:18973327
Hydrogen-bond detection, configuration assignment and rotamer correction of side-chain amides in large proteins by NMR spectroscopy through protium/deuterium isotope effects. PMID:18973166
The ConSurf-DB: pre-calculated evolutionary conservation profiles of protein structures. PMID:18971256
Dibutyltin disrupts glucocorticoid receptor function and impairs glucocorticoid-induced suppression of cytokine production. PMID:18958157
APD2: the updated antimicrobial peptide database and its application in peptide design. PMID:18957441
A knowledge-based structure-discriminating function that requires only main-chain atom coordinates. PMID:18957132
Rfam: updates to the RNA families database. PMID:18953034
Consensus prediction of protein conformational disorder from amino acidic sequence. PMID:18949069
A comparative analysis of viral matrix proteins using disorder predictors. PMID:18947403
SPROUTS: a database for the evaluation of protein stability upon point mutation. PMID:18945702
Distinct structural elements dictate the specificity of the type III pentaketide synthase from Neurospora crassa. PMID:18940668
Recognition of the activated states of Galpha13 by the rgRGS domain of PDZRhoGEF. PMID:18940608
Volume-based solvation models out-perform area-based models in combined studies of wild-type and mutated protein-protein interfaces. PMID:18939984
MMsINC: a large-scale chemoinformatics database. PMID:18931373
Nanotechnology, nanotoxicology, and neuroscience. PMID:18926873
AMMOS: Automated Molecular Mechanics Optimization tool for in silico Screening. PMID:18925937
Molecular characterization and expression analysis of beta2-microglobulin in large yellow croaker Pseudosciaena crocea. PMID:18853280
Protein docking by the underestimation of free energy funnels in the space of encounter complexes. PMID:18846200
BPS: a database of RNA base-pair structures. PMID:18845572
Homology modelling of protein-protein complexes: a simple method and its possibilities and limitations. PMID:18844985
Potent HIV-1 protease inhibitors incorporating meso-bicyclic urethanes as P2-ligands: structure-based design, synthesis, biological evaluation and protein-ligand X-ray studies. PMID:18843400
CPDB: a database of circular permutation in proteins. PMID:18842637
Side-chain conformational space analysis (SCSA): a multi conformation-based QSAR approach for modeling and prediction of protein-peptide binding affinities. PMID:18841329
Structural segments and residue propensities in protein-RNA interfaces: comparison with protein-protein and protein-DNA complexes. PMID:18841236
Probing the origin of tubulin rigidity with molecular simulations. PMID:18840679
The apolar channel in Cerebratulus lacteus hemoglobin is the route for O2 entry and exit. PMID:18840607
Identification of new, well-populated amino-acid sidechain rotamers involving hydroxyl-hydrogen atoms and sulfhydryl-hydrogen atoms. PMID:18840291
The interactome: predicting the protein-protein interactions in cells. PMID:18839074
PiSite: a database of protein interaction sites using multiple binding states in the PDB. PMID:18836195
Behavioral differences between phosphatidic acid and phosphatidylcholine in the presence of the nicotinic acetylcholine receptor. PMID:18835908
Discarding functional residues from the substitution table improves predictions of active sites within three-dimensional structures. PMID:18833291
How well can the accuracy of comparative protein structure models be predicted? PMID:18832340
Protein intrinsic disorder toolbox for comparative analysis of viral proteins. PMID:18831795
The FEATURE framework for protein function annotation: modeling new functions, improving performance, and extending to novel applications. PMID:18831785
Selective detection of protein crystals by second harmonic microscopy. PMID:18831587
Solution NMR structure determination of proteins revisited. PMID:18827972
Differences between high- and low-affinity complexes of enzymes and nonenzymes. PMID:18826206
Amino acid contacts in proteins adapted to different temperatures: hydrophobic interactions and surface charges play a key role. PMID:18825305
Analysis and classification of RNA tertiary structures. PMID:18824509
iRefIndex: a consolidated protein interaction database with provenance. PMID:18823568
Improving NMR protein structure quality by Rosetta refinement: a molecular replacement study. PMID:18816799
Directed evolution of a G protein-coupled receptor for expression, stability, and binding selectivity. PMID:18812512
Sexual and apomictic seed formation in Hieracium requires the plant polycomb-group gene FERTILIZATION INDEPENDENT ENDOSPERM. PMID:18812497
SSMap: a new UniProt-PDB mapping resource for the curation of structural-related information in the UniProt/Swiss-Prot Knowledgebase. PMID:18811932
pi-Turns: types, systematics and the context of their occurrence in protein structures. PMID:18808671
Automated structure determination from NMR spectra. PMID:18807026
Sequence based residue depth prediction using evolutionary information and predicted secondary structure. PMID:18803867
Computational structural analysis: multiple proteins bound to DNA. PMID:18802470
Protein-DNA interactions: structural, thermodynamic and clustering patterns of conserved residues in DNA-binding proteins. PMID:18801847
Autophosphorylation-induced degradation of the Pho85 cyclin Pcl5 is essential for response to amino acid limitation. PMID:18794371
Wanted: unique names for unique atom positions. PDB-wide analysis of diastereotopic atom names of small molecules containing diphosphate. PMID:18793461
Quantum chemical 13C(alpha) chemical shift calculations for protein NMR structure determination, refinement, and validation. PMID:18787110
Target flexibility: an emerging consideration in drug discovery and design. PMID:18785728
New insights into intra- and intermolecular interactions of immunoglobulins: crystal structure of mouse IgG2b-Fc at 2.1-A resolution. PMID:18783468
Flexible cyclic ethers/polyethers as novel P2-ligands for HIV-1 protease inhibitors: design, synthesis, biological evaluation, and protein-ligand X-ray studies. PMID:18783203
Performance of density functional models to reproduce observed (13)C(alpha) chemical shifts of proteins in solution. PMID:18780343
What induces pocket openings on protein surface patches involved in protein-protein interactions? PMID:18777159
Alpha-helical topology prediction and generation of distance restraints in membrane proteins. PMID:18775963
Mechanism of the chemical step for the guanosine triphosphate (GTP) hydrolysis catalyzed by elongation factor Tu. PMID:18773979
The GANC tetraloop: a novel motif in the group IIC intron structure. PMID:18773908
Insights into protein-DNA interactions through structure network analysis. PMID:18773096
Structure-based design of a T-cell receptor leads to nearly 100-fold improvement in binding affinity for pepMHC. PMID:18767161
Towards accurate residue-residue hydrophobic contact prediction for alpha helical proteins via integer linear optimization. PMID:18767158
Synthesis and SAR study of N-(4-hydroxy-3-(2-hydroxynaphthalene-1-yl)phenyl)-arylsulfonamides: heat shock protein 90 (Hsp90) inhibitors with submicromolar activity in an in vitro assay. PMID:18762423
Biomolecular pleiomorphism probed by spatial interpolation of coarse models. PMID:18757874
Built-in loops allow versatility in domain-domain interactions: lessons from self-interacting domains. PMID:18757736
Alignment of protein structures in the presence of domain motions. PMID:18727838
Estimates of natural selection due to protein tertiary structure inform the ancestry of biallelic loci. PMID:18725272
Optimal design of thermally stable proteins. PMID:18723523
Protein structure search and local structure characterization. PMID:18721472
Determining Rieske cluster reduction potentials. PMID:18719951
Iterative cluster-NMA: A tool for generating conformational transitions in proteins. PMID:18712827
RNase footprinting demonstrates antigenomic hepatitis delta virus ribozyme structural rearrangement as a result of self-cleavage reaction. PMID:18710542
Substrate binding pocket residues of human alkyladenine-DNA glycosylase critical for methylating agent survival. PMID:18706524
Information theory provides a comprehensive framework for the evaluation of protein structure predictions. PMID:18704942
A parasite cysteine protease is key to host protein degradation and iron acquisition. PMID:18701454
Neutrophil elastase reduces secretion of secretory leukoproteinase inhibitor (SLPI) by lung epithelial cells: role of charge of the proteinase-inhibitor complex. PMID:18699987
CHARMMing: a new, flexible web portal for CHARMM. PMID:18698840
Conservation and variability of dengue virus proteins: implications for vaccine design. PMID:18698358
HIV-1 capsid assembly inhibitor (CAI) peptide: structural preferences and delivery into human embryonic lung cells and lymphocytes. PMID:18695744
Natural/random protein classification models based on star network topological indices. PMID:18692072
BioJava: an open-source framework for bioinformatics. PMID:18689808
Evolutionary diversification of the Sm family of RNA-associated proteins. PMID:18687770
Automated clustering of probe molecules from solvent mapping of protein surfaces: new algorithms applied to hot-spot mapping and structure-based drug design. PMID:18679808
Chirality-based signatures of local protein environments in two-dimensional optical spectroscopy of two species photosynthetic complexes of green sulfur bacteria: simulation study. PMID:18676650
Proteopedia - a scientific 'wiki' bridging the rift between three-dimensional structure and function of biomacromolecules. PMID:18673581
Structure of AscE and induced burial regions in AscE and AscG upon formation of the chaperone needle-subunit complex of type III secretion system in Aeromonas hydrophila. PMID:18662905
Positional cloning of "Lisch-Like", a candidate modifier of susceptibility to type 2 diabetes in mice. PMID:18654634
Prediction by graph theoretic measures of structural effects in proteins arising from non-synonymous single nucleotide polymorphisms. PMID:18654622
Application of a polarizable force field to calculations of relative protein-ligand binding affinities. PMID:18653760
Predicting protein folding pathways at the mesoscopic level based on native interactions between secondary structure elements. PMID:18651953
Structure and mechanistic implications of a uroporphyrinogen III synthase-product complex. PMID:18651750
Crystal structure of the cell wall anchor domain of MotB, a stator component of the bacterial flagellar motor: implications for peptidoglycan recognition. PMID:18647830
Representation of viruses in the remediated PDB archive. PMID:18645236
Conformer selection and induced fit in flexible backbone protein-protein docking using computational and NMR ensembles. PMID:18640688
Catalytic cycle of human glutathione reductase near 1 A resolution. PMID:18638483
MSDmotif: exploring protein sites and motifs. PMID:18637174
Improving accuracy and efficiency of blind protein-ligand docking by focusing on predicted binding sites. PMID:18636505
Unfolding and melting of DNA (RNA) hairpins: the concept of structure-specific 2D dynamic landscapes. PMID:18633543
Identification and validation of human DNA ligase inhibitors using computer-aided drug design. PMID:18630893
ISMB 2003 Text Mining SIG Meeting Report. PMID:18629019
TEMBLOR - Perspectives of EBI Database Services. PMID:18628871
Processing of predicted substrates of fungal Kex2 proteinases from Candida albicans, C. glabrata, Saccharomyces cerevisiae and Pichia pastoris. PMID:18625069
The hemoglobins of the trematodes Fasciola hepatica and Paramphistomum epiclitum: a molecular biological, physico-chemical, kinetic, and vaccination study. PMID:18621914
Self-assembly of a simple membrane protein: coarse-grained molecular dynamics simulations of the influenza M2 channel. PMID:18621807
Bioinformatic method for protein thermal stabilization by structural entropy optimization. PMID:18621726
The high-affinity E. coli methionine ABC transporter: structure and allosteric regulation. PMID:18621668
Architectures and functional coverage of protein-protein interfaces. PMID:18620705
Rapid comparison of properties on protein surface. PMID:18618695
The Medium-Chain Dehydrogenase/reductase Engineering Database: a systematic analysis of a diverse protein family to understand sequence-structure-function relationship. PMID:18614751
Data mining of metal ion environments present in protein structures. PMID:18614239
Biomolecular simulation and modelling: status, progress and prospects. PMID:18611844
Metal ions in biological catalysis: from enzyme databases to general principles. PMID:18604568
Divalent metal ion complexes of S100B in the absence and presence of pentamidine. PMID:18602402
BCL::Align-sequence alignment and fold recognition with a custom scoring function online. PMID:18601985
3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures. PMID:18600227
Statistical analysis of interface similarity in crystals of homologous proteins. PMID:18599072
Molecular docking of cathepsin L inhibitors in the binding site of papain. PMID:18598021
Contextual specificity in peptide-mediated protein interactions. PMID:18596940
Molecular motions of human HIV-1 gp120 envelope glycoproteins. PMID:18594881
PRISM: protein-protein interaction prediction by structural matching. PMID:18592198
A protein functional leap: how a single mutation reverses the function of the transcription regulator TetR. PMID:18587152
MACHOS: Markov clusters of homologous subsequences. PMID:18586748
A computational framework to empower probabilistic protein design. PMID:18586717
Designing succinct structural alphabets. PMID:18586712
Structural basis of the transcriptional regulation of the proline utilization regulon by multifunctional PutA. PMID:18586269
Novel protein folds and their nonsequential structural analogs. PMID:18583523
Indel PDB: a database of structural insertions and deletions derived from sequence alignments of closely related proteins. PMID:18578882
Numbat: an interactive software tool for fitting Deltachi-tensors to molecular coordinates using pseudocontact shifts. PMID:18574699
Human Proteinpedia as a resource for clinical proteomics. PMID:18573810
YUP.SCX: coaxing atomic models into medium resolution electron density maps. PMID:18572416
Immunological hotspots analyzed by docking simulations: evidence for a general mechanism in pemphigus vulgaris pathology and transformation. PMID:18564435
Comparative structural dynamics of Tyrosyl-tRNA synthetase complexed with different substrates explored by molecular dynamics. PMID:18560823
Protein structure prediction using basin-hopping. PMID:18554063
Protein model refinement using an optimized physics-based all-atom force field. PMID:18550813
The torsin-family AAA+ protein OOC-5 contains a critical disulfide adjacent to Sensor-II that couples redox state to nucleotide binding. PMID:18550799
Mapping the nucleotide and isoform-dependent structural and dynamical features of Ras proteins. PMID:18547521
Hot-spot residues at the E9/Im9 interface help binding via different mechanisms. PMID:18546205
Onto-CC: a web server for identifying Gene Ontology conceptual clusters. PMID:18544607
X-ray structure of ILL2, an auxin-conjugate amidohydrolase from Arabidopsis thaliana. PMID:18543330
SiteSeek: post-translational modification analysis using adaptive locality-effective kernel methods and new profiles. PMID:18541042
Expression, purification, crystallization and preliminary X-ray analysis of Rv3117, a probable thiosulfate sulfurtransferase (CysA3) from Mycobacterium tuberculosis. PMID:18540071
KFC Server: interactive forecasting of protein interaction hot spots. PMID:18539611
A shotgun proteomic method for the identification of membrane-embedded proteins and peptides. PMID:18537282
Potato virus A genome-linked protein VPg is an intrinsically disordered molten globule-like protein with a hydrophobic core. PMID:18533220
Potent non-nucleoside inhibitors of the measles virus RNA-dependent RNA polymerase complex. PMID:18529043
SODa: an Mn/Fe superoxide dismutase prediction and design server. PMID:18518943
Immune epitope database analysis resource (IEDB-AR). PMID:18515843
Structural change in a B-DNA helix with hydrostatic pressure. PMID:18515837
Protein quaternary structure and expression levels contribute to peroxisomal-targeting-sequence-1-mediated peroxisomal import of human soluble epoxide hydrolase. PMID:18513744
Protein contact order prediction from primary sequences. PMID:18513429
Prediction of structural stability of short beta-hairpin peptides by molecular dynamics and knowledge-based potentials. PMID:18510728
Docking to RNA via root-mean-square-deviation-driven energy minimization with flexible ligands and flexible targets. PMID:18510306
Probing protein aggregation using discrete molecular dynamics. PMID:18508545
Conserved network properties of helical membrane protein structures and its implication for improving membrane protein homology modeling at the twilight zone. PMID:18506576
A reexamination of the propensities of amino acids towards a particular secondary structure: classification of amino acids based on their chemical structure. PMID:18504624
SCANPS: a web server for iterative protein sequence database searching by dynamic programing, with display in a hierarchical SCOP browser. PMID:18503088
Use of decoys to optimize an all-atom force field including hydration. PMID:18502794
SARSA: a web tool for structural alignment of RNA using a structural alphabet. PMID:18502774
Lysophospholipid interactions with protein targets. PMID:18501204
The use of local surface properties for molecular superimposition. PMID:18500543
Superimpose: a 3D structural superposition server. PMID:18492720
Protein-protein docking benchmark version 3.0. PMID:18491384
Ligand preference and orientation in b- and c-type heme-binding proteins. PMID:18491383
Structural evidence for lack of inhibition of fish goose-type lysozymes by a bacterial inhibitor of lysozyme. PMID:18491152
soaPDB: a web application for searching the Protein Data Bank, organizing results, and receiving automatic email alerts. PMID:18487276
Interactions between PBEF and oxidative stress proteins--a potential new mechanism underlying PBEF in the pathogenesis of acute lung injury. PMID:18486613
Prediction of membrane-protein topology from first principles. PMID:18477697
In pursuit of virtual lead optimization: the role of the receptor structure and ensembles in accurate docking. PMID:18473360
REACH coarse-grained biomolecular simulation: transferability between different protein structural classes. PMID:18469078
The beta-glucosidases responsible for bioactivation of hydroxynitrile glucosides in Lotus japonicus. PMID:18467457
A new peptide docking strategy using a mean field technique with mutually orthogonal Latin square sampling. PMID:18465087
IMGT, the International ImMunoGeneTics Information System for Immunoinformatics : methods for querying IMGT databases, tools, and web resources in the context of immunoinformatics. PMID:18463990
Computer-based screening of functional conformers of proteins. PMID:18463705
The Jpred 3 secondary structure prediction server. PMID:18463136
Interesting structures: education and outreach at the RCSB Protein Data Bank. PMID:18462020
De-orphaning the structural proteome through reciprocal comparison of evolutionarily important structural features. PMID:18461181
RAPIDO: a web server for the alignment of protein structures in the presence of conformational changes. PMID:18460546
Sequence specific resonance assignment via Multicanonical Monte Carlo search using an ABACUS approach. PMID:18458824
Structural characterization of the involvement of SigC in the regulation of the gene expression of pathogenic Mycobacterium ulcerans. PMID:18454323
Crystallization and preliminary crystallographic studies of Hyp-1, a St John's wort protein implicated in the biosynthesis of hypericin. PMID:18453712
Crystallization and preliminary characterization of a novel haem-binding protein of Streptomyces reticuli. PMID:18453708
Structure of a putative acetyltransferase (PA1377) from Pseudomonas aeruginosa. PMID:18453699
Inherited human cPLA(2alpha) deficiency is associated with impaired eicosanoid biosynthesis, small intestinal ulceration, and platelet dysfunction. PMID:18451993
Characterization and prediction of residues determining protein functional specificity. PMID:18450811
Cupin: a candidate molecular structure for the Nep1-like protein family. PMID:18447914
Revealing the moonlighting role of NADP in the structure of a flavin-containing monooxygenase. PMID:18443301
The RosettaDock server for local protein-protein docking. PMID:18442991
The twilight zone between protein order and disorder. PMID:18441033
Side-chain dynamics are critical for water permeation through aquaporin-1. PMID:18441032
Progress and challenges in protein structure prediction. PMID:18436442
Prevalence of intrinsic disorder in the intracellular region of human single-pass type I proteins: the case of the notch ligand Delta-4. PMID:18435556
Side chain substitution benchmark for peptide/MHC interaction. PMID:18434501
Structures, basins, and energies: a deconstruction of the Protein Coil Library. PMID:18434497
Structural and functional characterization of a novel phosphatase from the Arabidopsis thaliana gene locus At1g05000. PMID:18433060
Overview of protein structural and functional folds. PMID:18429251
Comparative protein structure modeling using Modeller. PMID:18428767
Multipattern consensus regions in multiple aligned protein sequences and their segmentation. PMID:18427583
FireDock: a web server for fast interaction refinement in molecular docking. PMID:18424796
Conformational isomerism can limit antibody catalysis. PMID:18417480
HIV-1 protease inhibitors from inverse design in the substrate envelope exhibit subnanomolar binding to drug-resistant variants. PMID:18412349
Crystal structures of a second g protein-coupled receptor: triumphs and implications. PMID:18409177
MS-DOCK: accurate multiple conformation generator and rigid docking protocol for multi-step virtual ligand screening. PMID:18402678
PSAIA - protein structure and interaction analyzer. PMID:18400099
Nature of protein family signatures: insights from singular value analysis of position-specific scoring matrices. PMID:18398479
Cloning, purification and preliminary X-ray analysis of the C-terminal domain of Helicobacter pylori MotB. PMID:18391426
Rethinking proteasome evolution: two novel bacterial proteasomes. PMID:18389302
FunClust: a web server for the identification of structural motifs in a set of non-homologous protein structures. PMID:18387204
Alignment of non-covalent interactions at protein-protein interfaces. PMID:18382693
A poke in the eye: inhibiting HIV-1 protease through its flap-recognition pocket. PMID:18381626
Protein sequence and structure alignments within one framework. PMID:18380904
Assessing side-chain perturbations of the protein backbone: a knowledge-based classification of residue Ramachandran space. PMID:18377931
Charge environments around phosphorylation sites in proteins. PMID:18366741
A multi-template combination algorithm for protein comparative modeling. PMID:18366648
Testing the Coulomb/Accessible Surface Area solvent model for protein stability, ligand binding, and protein design. PMID:18366628
Protein disorder prediction at multiple levels of sensitivity and specificity. PMID:18366622
A new paradigm for pattern recognition of drugs. PMID:18357415
Local knowledge helps determine protein structures. PMID:18353980
Versatile strategy for the synthesis of biotin-labelled glycans, their immobilization to establish a bioactive surface and interaction studies with a lectin on a biochip. PMID:18347977
Characterization of a complete cycle of acetylcholinesterase catalysis by ab initio QM/MM modeling. PMID:18343962
Modeling dimerizations of transmembrane proteins using Brownian dynamics simulations. PMID:18338226
Dynamics of Recognition between tRNA and elongation factor Tu. PMID:18336835
SHEF: a vHTS geometrical filter using coefficients of spherical harmonic molecular surfaces. PMID:18330602
Observation of noncooperative folding thermodynamics in simulations of 1BBL. PMID:18326644
ComPath: comparative enzyme analysis and annotation in pathway/subsystem contexts. PMID:18325116
The war of tools: how can NMR spectroscopists detect errors in their structures? PMID:18320330
Automated 3D phenotype analysis using data mining. PMID:18320060
Tandem duplication, circular permutation, molecular adaptation: how Solanaceae resist pests via inhibitors. PMID:18315854
Modelling the structures of G protein-coupled receptors aided by three-dimensional validation. PMID:18315845
Improved general regression network for protein domain boundary prediction. PMID:18315843
Analyzing the simplicial decomposition of spatial protein structures. PMID:18315842
Protein conformational flexibility prediction using machine learning. PMID:18313957
Structural studies of thiamin monophosphate kinase in complex with substrates and products. PMID:18311927
Protein dynamics and stability: the distribution of atomic fluctuations in thermophilic and mesophilic dihydrofolate reductase derived using elastic incoherent neutron scattering. PMID:18310248
Being a binding site: characterizing residue composition of binding sites on proteins. PMID:18305831
Structural and numerical variation of FLT3/ITD in pediatric AML. PMID:18305215
Assessing the solvent-dependent surface area of unfolded proteins using an ensemble model. PMID:18305164
Mapping of immunogenic and protein-interacting regions at the surface of the seven-bladed beta-propeller domain of the HIV-1 cellular interactor EED. PMID:18302803
Effect of low-complexity regions on protein structure determination. PMID:18302007
A template-finding algorithm and a comprehensive benchmark for homology modeling of proteins. PMID:18300226
On the relation between the predicted secondary structure and the protein size. PMID:18299971
Characterisation of transition state structures for protein folding using 'high', 'medium' and 'low' {Phi}-values. PMID:18299294
Q-Dock: Low-resolution flexible ligand docking with pocket-specific threading restraints. PMID:18293308
Three dimensional modeling of N-terminal region of galanin and its interaction with the galanin receptor. PMID:18288336
FGO: a novel ontology for identification of ligand functional group. PMID:18288335
Accurate structural correlations from maximum likelihood superpositions. PMID:18282091
Predicting RNA-binding sites from the protein structure based on electrostatics, evolution and geometry. PMID:18276647
The application of FAST-NMR for the identification of novel drug discovery targets. PMID:18275915
Close correspondence between the motions from principal component analysis of multiple HIV-1 protease structures and elastic network modes. PMID:18275822
Community benchmarks for virtual screening. PMID:18273555
Role of Mg2+ in hammerhead ribozyme catalysis from molecular simulation. PMID:18271579
Analysis of the human kinome using methods including fold recognition reveals two novel kinases. PMID:18270584
A novel Cas family member, HEPL, regulates FAK and cell spreading. PMID:18256281
Functional importance of individual rRNA 2'-O-ribose methylations revealed by high-resolution phenotyping. PMID:18256246
Kinetic, thermodynamic and X-ray structural insights into the interaction of melatonin and analogues with quinone reductase 2. PMID:18254726
Structure of the N-terminal region of complement factor H and conformational implications of disease-linked sequence variations. PMID:18252712
Adaptive functional divergence among triplicated alpha-globin genes in rodents. PMID:18245844
Homology modeling of 5-lipoxygenase and hints for better inhibitor design. PMID:18231862
From knotted to nested RNA structures: a variety of computational methods for pseudoknot removal. PMID:18230758
Intrinsic evaluation of text mining tools may not predict performance on realistic tasks. PMID:18229722
Striking similarities in diverse telomerase proteins revealed by combining structure prediction and machine learning approaches. PMID:18229711
Involvement of DPP-IV catalytic residues in enzyme-saxagliptin complex formation. PMID:18227430
Restricted mobility of conserved residues in protein-protein interfaces in molecular simulations. PMID:18227135
A comprehensive analysis of the thermodynamic events involved in ligand-receptor binding using CoRIA and its variants. PMID:18219446
A dynamic Bayesian network approach to protein secondary structure prediction. PMID:18218144
How to do an evaluation: pitfalls and traps. PMID:18217218
A ligand's-eye view of protein binding. PMID:18217215
I-TASSER server for protein 3D structure prediction. PMID:18215316
A combination of rescoring and refinement significantly improves protein docking performance. PMID:18214977
Gene characterization index: assessing the depth of gene annotation. PMID:18213364
Analysis of self-associating proteins by singular value decomposition of solution scattering data. PMID:18212017
CPSARST: an efficient circular permutation search tool applied to the detection of novel protein structural relationships. PMID:18201387
Fast procedure for reconstruction of full-atom protein models from reduced representations. PMID:18196502
Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection--what can we learn from earlier mistakes? PMID:18196462
Evaluating docking programs: keeping the playing field level. PMID:18196461
Conserved water molecules stabilize the Omega-loop in class A beta-lactamases. PMID:18195065
RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution). PMID:18192612
Effects of posttranslational modifications on the structure and dynamics of histone H3 N-terminal Peptide. PMID:18192367
Prediction of enzyme function based on 3D templates of evolutionarily important amino acids. PMID:18190718
Archaeal protoglobin structure indicates new ligand diffusion paths and modulation of haem-reactivity. PMID:18188182
On the inhibitory affect of some dementia drugs on DNA polymerase Beta activity. PMID:18185993
Can we use docking and scoring for hit-to-lead optimization? PMID:18183356
Development of a physics-based force field for the scoring and refinement of protein models. PMID:18178653
Multiple-step virtual screening using VSM-G: overview and validation of fast geometrical matching enrichment. PMID:18172702
A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation. PMID:18165317
Molecular docking studies on tetrahydroimidazo-[4,5,1-jk][1,4]-benzodiazepinone (TIBO) derivatives as HIV-1 NNRT inhibitors. PMID:18163186
Background frequencies for residue variability estimates: BLOSUM revisited. PMID:18162129
Structural insights into RNA-dependent eukaryal and archaeal selenocysteine formation. PMID:18158303
Crystal structure of 5-methylthioribose 1-phosphate isomerase product complex from Bacillus subtilis: implications for catalytic mechanism. PMID:18156470
Identification of transient hub proteins and the possible structural basis for their multiple interactions. PMID:18156468
Userscripts for the life sciences. PMID:18154664
Estimating the length of transmembrane helices using Z-coordinate predictions. PMID:18096645
The JCSG MR pipeline: optimized alignments, multiple models and parallel searches. PMID:18094477
BALBES: a molecular-replacement pipeline. PMID:18094476
Surprises and pitfalls arising from (pseudo)symmetry. PMID:18094473
Crystallographic characterization of two novel crystal forms of human insulin induced by chaotropic agents and a shift in pH. PMID:18093308
Low oxygen affinity in reptilian hemoglobin D: prediction of residue interactions in Geochelone carbonaria HbD by homology modeling. PMID:18085430
Virtual screening for the discovery of bioactive natural products. PMID:18084917
STITCH: interaction networks of chemicals and proteins. PMID:18084021
Two-dimensional infrared spectroscopy as a probe of the solvent electrostatic field for a twelve residue peptide. PMID:18078331
Localizing frustration in native proteins and protein assemblies. PMID:18077414
Homology modeling of hemagglutinin/protease [HA/P (vibriolysin)] from Vibrio cholerae: sequence comparision, residue interactions and molecular mechanism. PMID:18074211
Exchanging murine and human immunoglobulin constant chains affects the kinetics and thermodynamics of antigen binding and chimeric antibody autoreactivity. PMID:18074033
Remediation of the protein data bank archive. PMID:18073189
Predicting gene ontology functions from protein's regional surface structures. PMID:18070366
Stereochemical criteria for prediction of the effects of proline mutations on protein stability. PMID:18069886
Selecting folded proteins from a library of secondary structural elements. PMID:18067292
Yeast as a model of human mitochondrial tRNA base substitutions: investigation of the molecular basis of respiratory defects. PMID:18065717
The code-based physics of formation of alpha-helices and beta-hairpins in water-soluble proteins. PMID:18064823
Characterization of a human coagulation factor Xa-binding site on Viperidae snake venom phospholipases A2 by affinity binding studies and molecular bioinformatics. PMID:18062812
A knowledge-based approach to generating diverse but energetically representative ensembles of ligand conformers. PMID:18058240
Binding of puerarin to human serum albumin: a spectroscopic analysis and molecular docking. PMID:18058205
Osmotic stress and viscous retardation of the Na,K-ATPase ion pump. PMID:18055532
Binding MOAD, a high-quality protein-ligand database. PMID:18055497
NMR and X-ray analysis of structural additivity in metal binding site-swapped hybrids of rubredoxin. PMID:18053245
CATHEDRAL: a fast and effective algorithm to predict folds and domain boundaries from multidomain protein structures. PMID:18052539
Draft crystal structure of the vault shell at 9-A resolution. PMID:18044992
Robust recognition of zinc binding sites in proteins. PMID:18042678
Identification of DNA-binding proteins using support vector machines and evolutionary profiles. PMID:18042272
STRALCP--structure alignment-based clustering of proteins. PMID:18039711
The Pfam protein families database. PMID:18039703
PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites. PMID:18039369
CancerLectinDB: a database of lectins relevant to cancer. PMID:18038206
Ligand discovery and virtual screening using the program LIDAEUS. PMID:18037921
Evaluating the protein coding potential of exonized transposable element sequences. PMID:18036258
A focused antibody library for selecting scFvs expressed at high levels in the cytoplasm. PMID:18034894
Protein crystallography for non-crystallographers, or how to get the best (but not more) from published macromolecular structures. PMID:18034855
Computational study on mechanism of G-quartet oligonucleotide T40214 selectively targeting Stat3. PMID:18034310
Distortion of flavin geometry is linked to ligand binding in cholesterol oxidase. PMID:18029419
Impact of DNA hairpin folding energetics on antibody-ssDNA association. PMID:18028946
KNOTTIN: the knottin or inhibitor cystine knot scaffold in 2007. PMID:18025039
Substrate binding and formation of an occluded state in the leucine transporter. PMID:18024499
Transcription processing at 1,N2-ethenoguanine by human RNA polymerase II and bacteriophage T7 RNA polymerase. PMID:18022639
Computationally mapping sequence space to understand evolutionary protein engineering. PMID:18020358
On macromolecular refinement at subatomic resolution with interatomic scatterers. PMID:18007035
Determination and validation of principal gene products. PMID:18006548
Complex of a protective antibody with its Ebola virus GP peptide epitope: unusual features of a V lambda x light chain. PMID:18005986
Sequence-similar, structure-dissimilar protein pairs in the PDB. PMID:18004789
Evaluating the potency of HIV-1 protease drugs to combat resistance. PMID:18004760
Structural basis for catalysis by onconase. PMID:18001769
Data growth and its impact on the SCOP database: new developments. PMID:18000004
The Proteomic Code: a molecular recognition code for proteins. PMID:17999762
Improving model construction of profile HMMs for remote homology detection through structural alignment. PMID:17999748
Structural mapping of protein interactions reveals differences in evolutionary pressures correlated to mRNA level and protein abundance. PMID:17997970
Increased catalytic efficiency following gene fusion of bifunctional methionine sulfoxide reductase enzymes from Shewanella oneidensis. PMID:17997579
Using molecular principal axes for structural comparison: determining the tertiary changes of a FAB antibody domain induced by antigenic binding. PMID:17996091
Iron-sulfur protein folds, iron-sulfur chemistry, and evolution. PMID:17992543
NMR spectroscopic and analytical ultracentrifuge analysis of membrane protein detergent complexes. PMID:17988403
BioMagResBank. PMID:17984079
Detecting coevolution in and among protein domains. PMID:17983264
IDBD: infectious disease biomarker database. PMID:17982173
SABERTOOTH: protein structural alignment based on a vectorial structure representation. PMID:17974011
Gene identification and structural characterization of the pyridoxal 5'-phosphate degradative protein 3-hydroxy-2-methylpyridine-4,5-dicarboxylate decarboxylase from mesorhizobium loti MAFF303099. PMID:17973403
Identification of GATC- and CCGG-recognizing Type II REases and their putative specificity-determining positions using Scan2S--a novel motif scan algorithm with optional secondary structure constraints. PMID:17972284
A Brownian Dynamics computational study of the interaction of spinach plastocyanin with turnip cytochrome f: the importance of plastocyanin conformational changes. PMID:17972160
The tertiary structure and domain organization of coagulation factor VIII. PMID:17965321
Monte Carlo refinement of rigid-body protein docking structures with backbone displacement and side-chain optimization. PMID:17965193
ProCKSI: a decision support system for Protein (structure) Comparison, Knowledge, Similarity and Information. PMID:17963510
The challenge of protein structure determination--lessons from structural genomics. PMID:17962404
Pharmacophore modeling and parallel screening for PPAR ligands. PMID:17960326
Structural motifs of biomolecules. PMID:17959779
Picosecond fluctuating protein energy landscape mapped by pressure temperature molecular dynamics simulation. PMID:17956984
Coevolutionary patterns in cytochrome c oxidase subunit I depend on structural and functional context. PMID:17955155
Multiplicity of carbohydrate-binding sites in beta-prism fold lectins: occurrence and possible evolutionary implications. PMID:17954971
Novel cargo-binding site in the beta and delta subunits of coatomer. PMID:17954604
Solvent reaction field potential inside an uncharged globular protein: a bridge between implicit and explicit solvent models? PMID:17949217
Measuring nanometer distances in nucleic acids using a sequence-independent nitroxide probe. PMID:17947978
RNAJunction: a database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesign. PMID:17947325
CMGSDB: integrating heterogeneous Caenorhabditis elegans data sources using compositional data mining. PMID:17942411
Molecular evolution of the human SRPX2 gene that causes brain disorders of the Rolandic and Sylvian speech areas. PMID:17942002
Characterization of protein hubs by inferring interacting motifs from protein interactions. PMID:17941705
The 1.3 A resolution structure of the RNA tridecamer r(GCGUUUGAAACGC): metal ion binding correlates with base unstacking and groove contraction. PMID:17940138
DNA indels in coding regions reveal selective constraints on protein evolution in the human lineage. PMID:17935613
Development of a heme protein structure-electrochemical function database. PMID:17933771
LigASite--a database of biologically relevant binding sites in proteins with known apo-structures. PMID:17933762
Structural and transcriptional analyses of a purine nucleotide-binding protein from Pyrococcus furiosus: a component of a novel, membrane-bound multiprotein complex unique to this hyperthermophilic archaeon. PMID:17932790
Molecular docking identifies the binding of 3-chloropyridine moieties specifically to the S1 pocket of SARS-CoV Mpro. PMID:17931870
PFAAT version 2.0: a tool for editing, annotating, and analyzing multiple sequence alignments. PMID:17931421
Detailed estimation of bioinformatics prediction reliability through the Fragmented Prediction Performance Plots. PMID:17931407
Ligand-escape pathways from the ligand-binding domain of PPARgamma receptor as probed by molecular dynamics simulations. PMID:17929009
Spatial chemical conservation of hot spot interactions in protein-protein complexes. PMID:17925020
A theoretical study of zinc(II) interactions with amino acid models and peptide fragments. PMID:17924152
Structural disorder promotes assembly of protein complexes. PMID:17922903
TOPDB: topology data bank of transmembrane proteins. PMID:17921502
RNA FRABASE version 1.0: an engine with a database to search for the three-dimensional fragments within RNA structures. PMID:17921499
Bis-methionyl coordination in the crystal structure of the heme-binding domain of the streptococcal cell surface protein Shp. PMID:17920629
Synonymous codon usage in different protein secondary structural classes of human genes: implication for increased non-randomness of GC3 rich genes towards protein stability. PMID:17914237
Protein mechanics: a route from structure to function. PMID:17914231
DOMINE: a database of protein domain interactions. PMID:17913741
Antibody-protein interactions: benchmark datasets and prediction tools evaluation. PMID:17910770
M-TASSER: an algorithm for protein quaternary structure prediction. PMID:17905848
Enhancing the stability and solubility of TEV protease using in silico design. PMID:17905838
New protein fold revealed by a 1.65 A resolution crystal structure of Francisella tularensis pathogenicity island protein IglC. PMID:17905833
Identification of DNA-binding protein target sequences by physical effective energy functions: free energy analysis of lambda repressor-DNA complexes. PMID:17900341
Cellular expression and crystal structure of the murine cytomegalovirus major histocompatibility complex class I-like glycoprotein, m153. PMID:17897947
Linking microarray reporters with protein functions. PMID:17897448
Direct observation of ligand transfer and bond formation in cytochrome c oxidase by using mid-infrared chirped-pulse upconversion. PMID:17895387
Signal propagation in proteins and relation to equilibrium fluctuations. PMID:17892319
Single-molecule imaging and fluorescence lifetime imaging microscopy show different structures for high- and low-affinity epidermal growth factor receptors in A431 cells. PMID:17890389
Functional dissection of naturally occurring amino acid substitutions in eIF4E that confers recessive potyvirus resistance in plants. PMID:17890375
PocketPicker: analysis of ligand binding-sites with shape descriptors. PMID:17880740
HLA alleles associated with slow progression to AIDS truly prefer to present HIV-1 p24. PMID:17878955
Covariance NMR in higher dimensions: application to 4D NOESY spectroscopy of proteins. PMID:17876709
Toward Mycobacterium tuberculosis DXR inhibitor design: homology modeling and molecular dynamics simulations. PMID:17874041
Protein folding in membranes: insights from neutron diffraction studies of a membrane beta-sheet oligomer. PMID:17872952
InSite: a computational method for identifying protein-protein interaction binding sites on a proteome-wide scale. PMID:17868464
N-glycolyl GM1 ganglioside as a receptor for simian virus 40. PMID:17855525
Characterization of protein-protein interfaces. PMID:17851740
Between order and disorder in protein structures: analysis of "dual personality" fragments in proteins. PMID:17850753
Identification of high affinity fatty acid binding sites on human serum albumin by MM-PBSA method. PMID:17827235
How a vicinal layer of solvent modulates the dynamics of proteins. PMID:17827218
Molecular model of the outward facing state of the human P-glycoprotein (ABCB1), and comparison to a model of the human MRP5 (ABCC5). PMID:17803828
Preference of small molecules for local minimum conformations when binding to proteins. PMID:17786192
The anatomy of microbial cell state transitions in response to oxygen. PMID:17785531
A new crystal form of bovine pancreatic RNase A in complex with 2'-deoxyguanosine-5'-monophosphate. PMID:17768339
Modeling mutations in protein structures. PMID:17766392
Amino-acid interactions in psychrophiles, mesophiles, thermophiles, and hyperthermophiles: insights from the quasi-chemical approximation. PMID:17766385
The crystal structure of the ligand-binding module of human TAG-1 suggests a new mode of homophilic interaction. PMID:17766378
Intrinsic curvature of DNA influences LacR-mediated looping. PMID:17766355
Mechanism of auxin interaction with Auxin Binding Protein (ABP1): a molecular dynamics simulation study. PMID:17766341
Strong and weak hydrogen bonds in drug-DNA complexes: a statistical analysis. PMID:17762141
Automatic generation of 3D motifs for classification of protein binding sites. PMID:17760982
Loop modeling: Sampling, filtering, and scoring. PMID:17729286
Visualization software for molecular assemblies. PMID:17728125
Versatile annotation and publication quality visualization of protein complexes using POLYVIEW-3D. PMID:17727718
Spectrum of disease-causing mutations in protein secondary structures. PMID:17727703
Dynamic behavior of an intrinsically unstructured linker domain is conserved in the face of negligible amino acid sequence conservation. PMID:17721672
Setting up a large set of protein-ligand PDB complexes for the development and validation of knowledge-based docking algorithms. PMID:17718923
Convergent algorithms for protein structural alignment. PMID:17714583
The Extent of Cooperativity of Protein Motions Observed with Elastic Network Models Is Similar for Atomic and Coarser-Grained Models. PMID:17710199
Evaluating and learning from RNA pseudotorsional space: quantitative validation of a reduced representation for RNA structure. PMID:17707400
An integrative in silico approach for discovering candidates for drug-targetable protein-protein interactions in interactome data. PMID:17705877
Stretching to understand proteins - a survey of the protein data bank. PMID:17704142
Mechanism of inhibition of human secretory phospholipase A2 by flavonoids: rationale for lead design. PMID:17701137
Potent new antiviral compound shows similar inhibition and structural interactions with drug resistant mutants and wild type HIV-1 protease. PMID:17696515
Structure and sodium channel activity of an excitatory I1-superfamily conotoxin. PMID:17696362
FR3D: finding local and composite recurrent structural motifs in RNA 3D structures. PMID:17694311
Coarse-grained biomolecular simulation with REACH: realistic extension algorithm via covariance Hessian. PMID:17693469
Structure of a lectin from Canavalia gladiata seeds: new structural insights for old molecules. PMID:17683532
Insights into the biology of Escherichia coli through structural proteomics. PMID:17668295
Domain selection combined with improved cloning strategy for high throughput expression of higher eukaryotic proteins. PMID:17663785
Recognizing protein-protein interfaces with empirical potentials and reduced amino acid alphabets. PMID:17662112
Consensus Data Mining (CDM) Protein Secondary Structure Prediction Server: combining GOR V and Fragment Database Mining (FDM). PMID:17660202
The solution structure of ParD, the antidote of the ParDE toxin antitoxin module, provides the structural basis for DNA and toxin binding. PMID:17656583
Building native protein conformation from NMR backbone chemical shifts using Monte Carlo fragment assembly. PMID:17656574
A comparative analysis of the triloops in all high-resolution RNA structures reveals sequence structure relationships. PMID:17652406
The functional modulation of epigenetic regulators by alternative splicing. PMID:17651478
Outliers in SAR and QSAR: 2. Is a flexible binding site a possible source of outliers? PMID:17646926
Design of protein membrane interaction inhibitors by virtual ligand screening, proof of concept with the C2 domain of factor V. PMID:17646652
Bayesian refinement of protein functional site matching. PMID:17640336
Influence of water clustering on the dynamics of hydration water at the surface of a lysozyme. PMID:17631539
Identification of sensory and signal-transducing domains in two-component signaling systems. PMID:17628134
Dispersion terms and analysis of size- and charge dependence in an enhanced Poisson-Boltzmann approach. PMID:17628098
Numerical integration techniques for curved-element discretizations of molecule-solvent interfaces. PMID:17627358
Cryo-electron microscopy study of bacteriophage T4 displaying anthrax toxin proteins. PMID:17624389
Molecular evolution and functional divergence of the Ca(2+) sensor protein in store-operated Ca(2+) entry: stromal interaction molecule. PMID:17622354
Protein backbone chemical shifts predicted from searching a database for torsion angle and sequence homology. PMID:17610132
Structural modules for receptor dimerization in the S-locus receptor kinase extracellular domain. PMID:17609367
The PICM chemical scanning method for identifying domain-domain and protein-protein interfaces: applications to the core signaling complex of E. coli chemotaxis. PMID:17609125
A topological algorithm for identification of structural domains of proteins. PMID:17608939
QM/MM linear response method distinguishes ligand affinities for closely related metalloproteins. PMID:17607744
Small but versatile: the extraordinary functional and structural diversity of the beta-grasp fold. PMID:17605815
The role of hydrophobic interactions in positioning of peripheral proteins in membranes. PMID:17603894
Affinity and specificity of protein U1A-RNA complex formation based on an additive component free energy model. PMID:17603075
Functional annotation strategy for protein structures. PMID:17597920
Molecular drug targets and structure based drug design: A holistic approach. PMID:17597912
Paradigm development: comparative and predictive 3D modeling of HIV-1 Virion Infectivity Factor (Vif). PMID:17597910
Binding site prediction of galanin peptide using evolutionary trace method. PMID:17597884
Computational screening of inhibitors for HIV-1 integrase using a receptor based pharmacophore model. PMID:17597868
Structural features differentiate the mechanisms between 2S (2 state) and 3S (3 state) folding homodimers. PMID:17597851
The network of sequence flow between protein structures. PMID:17596339
High-throughput identification of interacting protein-protein binding sites. PMID:17594507
Structure of pyrrolysyl-tRNA synthetase, an archaeal enzyme for genetic code innovation. PMID:17592110
Identification of hot regions in protein-protein interactions by sequential pattern mining. PMID:17570867
Learning biophysically-motivated parameters for alpha helix prediction. PMID:17570862
Accurate prediction of protein secondary structure and solvent accessibility by consensus combiners of sequence and structure information. PMID:17570843
Using structural motif descriptors for sequence-based binding site prediction. PMID:17570148
Assessment of conformational ensemble sizes necessary for specific resolutions of coverage of conformational space. PMID:17569521
Construction of a genome-scale structural map at single-nucleotide resolution. PMID:17568010
A high-throughput method for membrane protein solubility screening: the ultracentrifugation dispersity sedimentation assay. PMID:17567744
eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape. PMID:17567616
PrDOS: prediction of disordered protein regions from amino acid sequence. PMID:17567614
Combined quantum mechanical and molecular mechanical simulations of one- and two-electron reduction potentials of flavin cofactor in water, medium-chain acyl-CoA dehydrogenase, and cholesterol oxidase. PMID:17567113
A reduced amino acid alphabet for understanding and designing protein adaptation to mutation. PMID:17565494
Cloning, expression, purification, crystallization and preliminary X-ray analysis of Thermus aquaticus succinyl-CoA synthetase. PMID:17565180
Structure of O67745_AQUAE, a hypothetical protein from Aquifex aeolicus. PMID:17565173
Insights into equilibrium dynamics of proteins from comparison of NMR and X-ray data with computational predictions. PMID:17562320
Predicting 13Calpha chemical shifts for validation of protein structures. PMID:17558470
Deciphering protein dynamics from NMR data using explicit structure sampling and selection. PMID:17557784
Analysis of protein three-dimension structure using amino acids depths. PMID:17557208
DOMAC: an accurate, hybrid protein domain prediction server. PMID:17553833
siteFiNDER|3D: a web-based tool for predicting the location of functional sites in proteins. PMID:17553829
Structural variation governs substrate specificity for organic anion transporter (OAT) homologs. Potential remote sensing by OAT family members. PMID:17553798
A post-synaptic scaffold at the origin of the animal kingdom. PMID:17551586
The first agmatine/cadaverine aminopropyl transferase: biochemical and structural characterization of an enzyme involved in polyamine biosynthesis in the hyperthermophilic archaeon Pyrococcus furiosus. PMID:17545282
Structural characterization of ferric hemoglobins from three antarctic fish species of the suborder notothenioidei. PMID:17545238
Crystal structure of the ferritin from the hyperthermophilic archaeal anaerobe Pyrococcus furiosus. PMID:17541801
The selection of acceptable protein mutations. PMID:17540730
X-ray crystal structures of human immunodeficiency virus type 1 protease mutants complexed with atazanavir. PMID:17537865
StrBioLib: a Java library for development of custom computational structural biology applications. PMID:17537750
Chemogenomic approaches to rational drug design. PMID:17533416
SNAP: predict effect of non-synonymous polymorphisms on function. PMID:17526529
The electrostatic characteristics of G.U wobble base pairs. PMID:17526525
Molecular dynamics simulations of the native and partially folded states of ubiquitin: influence of methanol cosolvent, pH, and temperature on the protein structure and dynamics. PMID:17525462
The neurobiologist's guide to structural biology: a primer on why macromolecular structure matters and how to evaluate structural data. PMID:17521566
A systematic comparative and structural analysis of protein phosphorylation sites based on the mtcPTM database. PMID:17521420
Hinge Atlas: relating protein sequence to sites of structural flexibility. PMID:17519025
ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. PMID:17517781
COMPASS server for remote homology inference. PMID:17517780
M4T: a comparative protein structure modeling server. PMID:17517764
Chlorophyll ring deformation modulates Qy electronic energy in chlorophyll-protein complexes and generates spectral forms. PMID:17513370
Structure of GrlR and the implication of its EDED motif in mediating the regulation of type III secretion system in EHEC. PMID:17511515
Structure of the dimeric N-glycosylated form of fungal beta-N-acetylhexosaminidase revealed by computer modeling, vibrational spectroscopy, and biochemical studies. PMID:17509134
Binding induced conformational changes of proteins correlate with their intrinsic fluctuations: a case study of antibodies. PMID:17509130
Locally enhanced sampling molecular dynamics study of the dioxygen transport in human cytoglobin. PMID:17503097
LinkHub: a Semantic Web system that facilitates cross-database queries and information retrieval in proteomics. PMID:17493288
CrystTwiV: a webserver for automated phase extension and refinement in X-ray crystallography. PMID:17488848
PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. PMID:17488841
Berkeley Phylogenomics Group web servers: resources for structural phylogenomic analysis. PMID:17488835
Ab initio modeling of small proteins by iterative TASSER simulations. PMID:17488521
Characterization of molecular recognition features, MoRFs, and their binding partners. PMID:17488107
Evaluation of the utility of homology models in high throughput docking. PMID:17487515
RNABindR: a server for analyzing and predicting RNA-binding sites in proteins. PMID:17483510
Protein free energy landscapes remodeled by ligand binding. PMID:17483166
DBAli tools: mining the protein structure space. PMID:17478513
NQ-Flipper: recognition and correction of erroneous asparagine and glutamine side-chain rotamers in protein structures. PMID:17478502
QSCOP-BLAST--fast retrieval of quantified structural information for protein sequences of unknown structure. PMID:17478501
MODPROPEP: a program for knowledge-based modeling of protein-peptide complexes. PMID:17478500
PMG: online generation of high-quality molecular pictures and storyboarded animations. PMID:17478496
Conformational changes of glucose/galactose-binding protein illuminated by open, unliganded, and ultra-high-resolution ligand-bound structures. PMID:17473016
Structural bases for substrate recognition and activity in Meaban virus nucleoside-2'-O-methyltransferase. PMID:17473012
Relating destabilizing regions to known functional sites in proteins. PMID:17470296
Crystal structure of human arginase I complexed with thiosemicarbazide reveals an unusual thiocarbonyl mu-sulfide ligand in the binuclear manganese cluster. PMID:17469833
In silico prediction of SARS protease inhibitors by virtual high throughput screening. PMID:17461975
Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models. PMID:17452785
MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. PMID:17452350
vGNM: a better model for understanding the dynamics of proteins in crystals. PMID:17451743
Ty3 capsid mutations reveal early and late functions of the amino-terminal domain. PMID:17442718
Prediction of flexible/rigid regions from protein sequences using k-spaced amino acid pairs. PMID:17437643
Spectroscopic and structural study of proton and halide ion cooperative binding to gfp. PMID:17434942
A systematic bioinformatics approach for selection of epitope-based vaccine targets. PMID:17434154
Lesion specificity in the base excision repair enzyme hNeil1: modeling and dynamics studies. PMID:17432829
Local comparison of protein structures highlights cases of convergent evolution in analogous functional sites. PMID:17430569
Structure-dependent relationships between growth temperature of prokaryotes and the amino acid frequency in their proteins. PMID:17429573
Cysteine substitution mutants give structural insight and identify ATP binding and activation sites at P2X receptors. PMID:17428985
Insights into molecular medicine: development of new diagnostic and prognostic parameters. PMID:17427009
Peptide segments in protein-protein interfaces. PMID:17426384
ProRegIn: a regularity index for the selection of native-like tertiary structures of proteins. PMID:17426381
Polarizable atomic multipole solutes in a Poisson-Boltzmann continuum. PMID:17411115
Structural analysis of charge discrimination in the binding of inhibitors to human carbonic anhydrases I and II. PMID:17407288
Activation of biliverdin-IXalpha reductase by inorganic phosphate and related anions. PMID:17402939
RNABC: forward kinematics to reduce all-atom steric clashes in RNA backbone. PMID:17401565
Structural insight into repair of alkylated DNA by a new superfamily of DNA glycosylases comprising HEAT-like repeats. PMID:17395642
Mechanisms for stabilisation and the maintenance of solubility in proteins from thermophiles. PMID:17394655
Identification of amino acid residues at the active site of endosialidase that dissociate the polysialic acid binding and cleaving activities in Escherichia coli K1 bacteriophages. PMID:17394421
Mutational analysis of aspartoacylase: implications for Canavan disease. PMID:17391648
Functional anthology of intrinsic disorder. 1. Biological processes and functions of proteins with long disordered regions. PMID:17391014
Phosphorylation of IRF8 in a pre-associated complex with Spi-1/PU.1 and non-phosphorylated Stat1 is critical for LPS induction of the IL1B gene. PMID:17386941
Computational characterization and design of SARS coronavirus receptor recognition and antibody neutralization. PMID:17374510
Models for protein binding to calcium oxalate surfaces. PMID:17372730
The implications of alternative splicing in the ENCODE protein complement. PMID:17372197
Editing modifies the GABA(A) receptor subunit alpha3. PMID:17369310
Consensus sequences improve PSI-BLAST through mimicking profile-profile alignments. PMID:17369271
Computational simulation of interactions between SARS coronavirus spike mutants and host species-specific receptors. PMID:17368104
Growth of novel protein structural data. PMID:17360626
Homology modeling and molecular dynamics simulations of the glycine receptor ligand binding domain. PMID:17357155
Cytosolic 5'-triphosphate ended viral leader transcript of measles virus as activator of the RIG I-mediated interferon response. PMID:17356690
Conformational dynamics of the major yeast phosphatidylinositol transfer protein sec14p: insight into the mechanisms of phospholipid exchange and diseases of sec14p-like protein deficiencies. PMID:17344474
Structure and kinetics of monofunctional proline dehydrogenase from Thermus thermophilus. PMID:17344208
Structure and characterization of a novel chicken biotin-binding protein A (BBP-A). PMID:17343730
Crystallographic, thermodynamic, and molecular modeling studies of the mode of binding of oligosaccharides to the potent antiviral protein griffithsin. PMID:17340634
Comparison of protein structures by growing neighborhood alignments. PMID:17338826
Outliers in SAR and QSAR: is unusual binding mode a possible source of outliers? PMID:17334823
Improved estimation of ligand-macromolecule binding affinities by linear response approach using a combination of multi-mode MD simulation and QM/MM methods. PMID:17333483
Long-time molecular dynamics simulations of botulinum biotoxin type-A at different pH values and temperatures. PMID:17333307
Crystallization and preliminary X-ray diffraction studies of trypsin-like proteases from the gastric fluid of the marine crab Cancer pagurus. PMID:17329824
Crystallization and molecular-replacement solution of a diagnostic fluorescent dye in complex with a specific Fab fragment. PMID:17329818
Efficient optimization of crystallization conditions by manipulation of drop volume ratio and temperature. PMID:17327388
A milestoning study of the kinetics of an allosteric transition: atomically detailed simulations of deoxy Scapharca hemoglobin. PMID:17325010
The X-ray crystal structure of PA1607 from Pseudomonas aureginosa at 1.9 A resolution--a putative transcription factor. PMID:17322537
Structure and interactions of the first three RNA recognition motifs of splicing factor prp24. PMID:17320109
Blast sampling for structural and functional analyses. PMID:17319945
Crystallographic evidence for dioxygen interactions with iron proteins. PMID:17318598
Modeling RNA tertiary structure motifs by graph-grammars. PMID:17317683
EpitopeViewer: a Java application for the visualization and analysis of immune epitopes in the Immune Epitope Database and Analysis Resource (IEDB). PMID:17313688
Competitive inhibitors of the CphA metallo-beta-lactamase from Aeromonas hydrophila. PMID:17307979
Functional impact of missense variants in BRCA1 predicted by supervised learning. PMID:17305420
Crystal structure of Homo sapiens kynureninase. PMID:17300176
Screened nonbonded interactions in native proteins manipulate optimal paths for robust residue communication. PMID:17293401
Protein structural variation in computational models and crystallographic data. PMID:17292835
Electrostatic control of the overall shape of calmodulin: numerical calculations. PMID:17285296
CoMSIA and docking study of rhenium based estrogen receptor ligand analogs. PMID:17280694
A molecular modeling study on the enantioselectivity of aryl alkyl ketone reductions by a NADPH-dependent carbonyl reductase. PMID:17279371
Energetics of protein-DNA interactions. PMID:17259221
Prediction of desmoglein-3 peptides reveals multiple shared T-cell epitopes in HLA DR4- and DR6-associated pemphigus vulgaris. PMID:17254312
Improving the performance of DomainDiscovery of protein domain boundary assignment using inter-domain linker index. PMID:17254311
Projections for fast protein structure retrieval. PMID:17254310
Highly potent triazole-based tubulin polymerization inhibitors. PMID:17249649
Ab initio molecular-replacement phasing for symmetric helical membrane proteins. PMID:17242512
Ligand configurational entropy and protein binding. PMID:17242351
Mouse SNP Miner: an annotated database of mouse functional single nucleotide polymorphisms. PMID:17239255
Beyond information retrieval--medical question answering. PMID:17238385
Using phylogeny to improve genome-wide distant homology recognition. PMID:17238281
Structure of the monooxygenase component of a two-component flavoprotein monooxygenase. PMID:17227849
Structural and functional characterization of the aryl hydrocarbon receptor ligand binding domain by homology modeling and mutational analysis. PMID:17223691
NMR structural characterization of substrates bound to N-acetylglucosaminyltransferase V. PMID:17204285
Direct observation in solution of a preexisting structural equilibrium for a mutant of the allosteric aspartate transcarbamoylase. PMID:17202260
GlycoMapsDB: a database of the accessible conformational space of glycosidic linkages. PMID:17202175
SNAPPI-DB: a database and API of Structures, iNterfaces and Alignments for Protein-Protein Interactions. PMID:17202171
REBASE--enzymes and genes for DNA restriction and modification. PMID:17202163
LigProf: a simple tool for in silico prediction of ligand-binding sites. PMID:17200839
A study of collective atomic fluctuations and cooperativity in the U1A-RNA complex based on molecular dynamics simulations. PMID:17194603
Prediction of structures of multidomain proteins from structures of the individual domains. PMID:17189483
Evolutionary conservation of domain-domain interactions. PMID:17184549
Multiple independent evolutionary solutions to core histone gene regulation. PMID:17184543
Observation of microsecond time-scale protein dynamics in the presence of Ln3+ ions: application to the N-terminal domain of cardiac troponin C. PMID:17180551
Interactions of the sweet protein brazzein with the sweet taste receptor. PMID:17177550
Stabilizing IkappaBalpha by "consensus" design. PMID:17174335
Photophysics of Clomeleon by FLIM: discriminating excited state reactions along neuronal development. PMID:17172293
T-B+NK+ severe combined immunodeficiency caused by complete deficiency of the CD3zeta subunit of the T-cell antigen receptor complex. PMID:17170122
Flexible segments modulate co-folding of dUTPase and nucleocapsid proteins. PMID:17169987
Evolutionary computation and multimodal search: a good combination to tackle molecular diversity in the field of peptide design. PMID:17165156
Ligand identification using electron-density map correlations. PMID:17164532
Macromolecular recognition in the Protein Data Bank. PMID:17164520
Catalytic activity, duplication and evolution of the CYP98 cytochrome P450 family in wheat. PMID:17160453
Evolution of the metazoan protein phosphatase 2C superfamily. PMID:17160364
On the characterization of protein native state ensembles. PMID:17158570
The structure of the minimal relaxase domain of MobA at 2.1 A resolution. PMID:17157875
Benchmarking sets for molecular docking. PMID:17154509
A Bayesian-probability-based method for assigning protein backbone dihedral angles based on chemical shifts and local sequences. PMID:17151953
Development and validation of a modular, extensible docking program: DOCK 5. PMID:17149653
The Molecular Biology Database Collection: 2007 update. PMID:17148484
Coverage of whole proteome by structural genomics observed through protein homology modeling database. PMID:17146617
Biochemical and structural characterization of the secreted chorismate mutase (Rv1885c) from Mycobacterium tuberculosis H37Rv: an *AroQ enzyme not regulated by the aromatic amino acids. PMID:17146044
The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation. PMID:17145713
BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities. PMID:17145705
The molecular structure of Rv1873, a conserved hypothetical protein from Mycobacterium tuberculosis, at 1.38 A resolution. PMID:17142896
On the decrease in lateral mobility of phospholipids by sugars. PMID:17142271
PolyDoms: a whole genome database for the identification of non-synonymous coding SNPs with the potential to impact disease. PMID:17142238
Phospho3D: a database of three-dimensional structures of protein phosphorylation sites. PMID:17142231
The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. PMID:17142228
Metalloprotein and metallo-DNA/RNAzyme design: current approaches, success measures, and future challenges. PMID:17140190
The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution. PMID:17135200
TransportDB: a comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channels. PMID:17135193
The interaction networks of structured RNAs. PMID:17135184
Rapid detection of similarity in protein structure and function through contact metric distances. PMID:17130161
Amino acid residue doublet propensity in the protein-RNA interface and its application to RNA interface prediction. PMID:17130160
Conformational specificity of non-canonical base pairs and higher order structures in nucleic acids: crystal structure database analysis. PMID:17124630
Efficient molecular docking of NMR structures: application to HIV-1 protease. PMID:17123961
Connectivity independent protein-structure alignment: a hierarchical approach. PMID:17118190
Sequence representation and prediction of protein secondary structure for structural motifs in twilight zone proteins. PMID:17115254
The cooperative response of synaptotagmin I C2A. A hypothesis for a Ca2+-driven molecular hammer. PMID:17114221
Novel methods for secondary structure determination using low wavelength (VUV) circular dichroism spectroscopic data. PMID:17112372
Milestones in electron crystallography. PMID:17103018
Identification and structural characterization of I84C and I84A mutations that are associated with high-level resistance to human immunodeficiency virus protease inhibitors and impair viral replication. PMID:17101675
EVEREST: a collection of evolutionary conserved protein domains. PMID:17099230
Modern proteomes contain putative imprints of ancient shifts in trace metal geochemistry. PMID:17098870
Predicting domain-domain interactions using a parsimony approach. PMID:17094802
DWARF--a data warehouse system for analyzing protein families. PMID:17094801
Identifying interaction sites in "recalcitrant" proteins: predicted protein and RNA binding sites in rev proteins of HIV-1 and EIAV agree with experimental data. PMID:17094257
Bhageerath: an energy based web enabled computer software suite for limiting the search space of tertiary structures of small globular proteins. PMID:17090600
Defensins knowledgebase: a manually curated database and information source focused on the defensins family of antimicrobial peptides. PMID:17090586
Database of traditional Chinese medicine and its application to studies of mechanism and to prescription validation. PMID:17088869
TMBETA-GENOME: database for annotated beta-barrel membrane proteins in genomic sequences. PMID:17088282
Membrane assembly of simple helix homo-oligomers studied via molecular dynamics simulations. PMID:17085501
MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms. PMID:17082206
Molecular dynamics simulations of RNA: an in silico single molecule approach. PMID:17080418
Crystallization and preliminary X-ray analysis of the aromatic prenyltransferase CloQ from the clorobiocin biosynthetic cluster of Streptomyces roseochromogenes. PMID:17077503
Sequence analysis and structure prediction of type II Pseudomonas sp. USM 4-55 PHA synthase and an insight into its catalytic mechanism. PMID:17076907
Orientation preferences of backbone secondary amide functional groups in peptide nucleic acid complexes: quantum chemical calculations reveal an intrinsic preference of cationic D-amino acid-based chiral PNA analogues for the P-form. PMID:17071666
Multiple, non-allelic, intein-coding sequences in eukaryotic RNA polymerase genes. PMID:17069655
A biocurator perspective: annotation at the Research Collaboratory for Structural Bioinformatics Protein Data Bank. PMID:17069453
Babel's tower revisited: a universal resource for cross-referencing across annotation databases. PMID:17068090
Crystallization and preliminary X-ray analysis of the aromatic prenyltransferase CloQ from the clorobiocin biosynthetic cluster of Streptomyces roseochromogenes. PMID:17077503
Sequence analysis and structure prediction of type II Pseudomonas sp. USM 4-55 PHA synthase and an insight into its catalytic mechanism. PMID:17076907
Orientation preferences of backbone secondary amide functional groups in peptide nucleic acid complexes: quantum chemical calculations reveal an intrinsic preference of cationic D-amino acid-based chiral PNA analogues for the P-form. PMID:17071666
Multiple, non-allelic, intein-coding sequences in eukaryotic RNA polymerase genes. PMID:17069655
A biocurator perspective: annotation at the Research Collaboratory for Structural Bioinformatics Protein Data Bank. PMID:17069453
Babel's tower revisited: a universal resource for cross-referencing across annotation databases. PMID:17068090
SISYPHUS--structural alignments for proteins with non-trivial relationships. PMID:17068077
Function and evolution of a gene family encoding odorant binding-like proteins in a social insect, the honey bee (Apis mellifera). PMID:17065610
TOPOFIT-DB, a database of protein structural alignments based on the TOPOFIT method. PMID:17065464
AcpA is a Francisella acid phosphatase that affects intramacrophage survival and virulence. PMID:17060465
Evolution of glyoxylate cycle enzymes in Metazoa: evidence of multiple horizontal transfer events and pseudogene formation. PMID:17059607
TOAC spin labels in the backbone of alamethicin: EPR studies in lipid membranes. PMID:17056731
Modeling and active site refinement for G protein-coupled receptors: application to the beta-2 adrenergic receptor. PMID:17054017
Development and application of hybrid structure based method for efficient screening of ligands binding to G-protein coupled receptors. PMID:17054015
Representing and comparing protein structures as paths in three-dimensional space. PMID:17052359
Efficient overlay of small organic molecules using 3D pharmacophores. PMID:17051340
An approach to crystallizing proteins by synthetic symmetrization. PMID:17050682
High-affinity binding of the staphylococcal HarA protein to haptoglobin and hemoglobin involves a domain with an antiparallel eight-stranded beta-barrel fold. PMID:17041047
Quantification and rationalization of the higher affinity of sodium over potassium to protein surfaces. PMID:17032760
Interrogating the druggable genome with structural informatics. PMID:17031532
Bayesian data mining of protein domains gives an efficient predictive algorithm and new insight. PMID:17028865
Mechanism of the difference in the binding affinity of E. coli tRNAGln to glutaminyl-tRNA synthetase caused by noninterface nucleotides in variable loop. PMID:17028132
Predicting residue-wise contact orders in proteins by support vector regression. PMID:17014735
Expression, purification, crystallization and preliminary X-ray analysis of two arginine-biosynthetic enzymes from Mycobacterium tuberculosis. PMID:17012791
Comparative residue interaction analysis (CoRIA): a 3D-QSAR approach to explore the binding contributions of active site residues with ligands. PMID:17009094
High-throughput structure-based pharmacophore modelling as a basis for successful parallel virtual screening. PMID:17009092
A combined ligand-based and target-based drug design approach for G-protein coupled receptors: application to salvinorin A, a selective kappa opioid receptor agonist. PMID:17009091
Thermodynamic basis for promiscuity and selectivity in protein-protein interactions: PDZ domains, a case study. PMID:17002371
A Consensus Data Mining secondary structure prediction by combining GOR V and Fragment Database Mining. PMID:17001039
A fast method for the determination of fractional contributions to solvation in proteins. PMID:17001031
Crystal structures of the DNA-binding domain of Escherichia coli proline utilization A flavoprotein and analysis of the role of Lys9 in DNA recognition. PMID:17001030
Taspine: bioactivity-guided isolation and molecular ligand-target insight of a potent acetylcholinesterase inhibitor from Magnolia x soulangiana. PMID:16989531
Crystal structure and activities of EXPB1 (Zea m 1), a beta-expansin and group-1 pollen allergen from maize. PMID:16984999
Dihedral-angle information entropy as a gauge of secondary structure propensity. PMID:16980371
Intricate knots in proteins: Function and evolution. PMID:16978047
Specificity of the VP1 GH loop of Foot-and-Mouth Disease virus for alphav integrins. PMID:16973584
PhyloFacts: an online structural phylogenomic encyclopedia for protein functional and structural classification. PMID:16973001
Do benzodiazepines mimic reverse-turn structures? PMID:16972167
Probing protein structure and dynamics by second-derivative ultraviolet absorption analysis of cation-{pi} interactions. PMID:16963649
TASSER-Lite: an automated tool for protein comparative modeling. PMID:16963505
CRYBA4, a novel human cataract gene, is also involved in microphthalmia. PMID:16960806
Quantitative analysis of the conservation of the tertiary structure of protein segments. PMID:16957991
Homocysteine thiolactone and human cholinesterases. PMID:16955366
Structural determinants for G-protein activation and specificity in the third intracellular loop of the thyroid-stimulating hormone receptor. PMID:16955277
Distill: a suite of web servers for the prediction of one-, two- and three-dimensional structural features of proteins. PMID:16953874
Co-evolutionary analysis of domains in interacting proteins reveals insights into domain-domain interactions mediating protein-protein interactions. PMID:16949097
Crystallization and preliminary crystallographic analysis of the tetrameric form of phosphofructokinase-2 from Escherichia coli, a member of the ribokinase family. PMID:16946484
Crystallization of mutant forms of glutaredoxin Grx1p from yeast. PMID:16946480
The purification, crystallization and preliminary structural characterization of PhzM, a phenazine-modifying methyltransferase from Pseudomonas aeruginosa. PMID:16946471
Structure of Bacillus halmapalus alpha-amylase crystallized with and without the substrate analogue acarbose and maltose. PMID:16946462
The folding mechanism of collagen-like model peptides explored through detailed molecular simulations. PMID:16943446
Configurational-bias sampling technique for predicting side-chain conformations in proteins. PMID:16943441
Homology modeling of tubulin: influence predictions for microtubule's biophysical properties. PMID:16941085
Oligomerization of hantavirus nucleocapsid protein: analysis of the N-terminal coiled-coil domain. PMID:16940519
Specific recognition of ZNF217 and other zinc finger proteins at a surface groove of C-terminal binding proteins. PMID:16940172
Dynamic switching mechanisms in LOV1 and LOV2 domains of plant phototropins. PMID:16935961
Novel STAT1 alleles in otherwise healthy patients with mycobacterial disease. PMID:16934001
MultiSeq: unifying sequence and structure data for evolutionary analysis. PMID:16914055
Modeling the open and closed forms of GABAA receptor: analysis of ligand-receptor interactions for the GABA-binding site. PMID:16913422
Enantioselective substrate binding in a monooxygenase protein model by molecular dynamics and docking. PMID:16905618
Role of the AP2 beta-appendage hub in recruiting partners for clathrin-coated vesicle assembly. PMID:16903783
Protein binding site prediction using an empirical scoring function. PMID:16893954
Indications that "codon boundaries" are physico-chemically defined and that protein-folding information is contained in the redundant exon bases. PMID:16893453
Unbinding of retinoic acid from the retinoic acid receptor by random expulsion molecular dynamics. PMID:16891362
Two crystal structures of Trichoderma reesei hydrophobin HFBI--the structure of a protein amphiphile with and without detergent interaction. PMID:16882996
Residue centrality, functionally important residues, and active site shape: analysis of enzyme and non-enzyme families. PMID:16882992
Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of Rv2827c from Mycobacterium tuberculosis. PMID:16880548
Monoclinic crystal form of Aspergillus niger alpha-amylase in complex with maltose at 1.8 angstroms resolution. PMID:16880540
An amino acid "transmembrane tendency" scale that approaches the theoretical limit to accuracy for prediction of transmembrane helices: relationship to biological hydrophobicity. PMID:16877712
Crystal structure of nonstructural protein 10 from the severe acute respiratory syndrome coronavirus reveals a novel fold with two zinc-binding motifs. PMID:16873246
Hydrogen tunnelling in enzyme-catalysed H-transfer reactions: flavoprotein and quinoprotein systems. PMID:16873125
A critical beta6-beta7 loop in the pleckstrin homology domain of ceramide kinase. PMID:16872273
Automated ligand fitting by core-fragment fitting and extension into density. PMID:16855309
Comprehensive evaluation of solution nuclear magnetic resonance spectroscopy sample preparation for helical integral membrane proteins. PMID:16850177
A global topology map of the Saccharomyces cerevisiae membrane proteome. PMID:16847258
OPAAS: a web server for optimal, permuted, and other alternative alignments of protein structures. PMID:16845117
FeatureMap3D--a tool to map protein features and sequence conservation onto homologous structures in the PDB. PMID:16845115
Protein Peeling 2: a web server to convert protein structures into series of protein units. PMID:16845113
FOLD-RATE: prediction of protein folding rates from amino acid sequence. PMID:16845101
SNP@Domain: a web resource of single nucleotide polymorphisms (SNPs) within protein domain structures and sequences. PMID:16845090
PREDITOR: a web server for predicting protein torsion angle restraints. PMID:16845087
New Onto-Tools: Promoter-Express, nsSNPCounter and Onto-Translate. PMID:16845086
UMMS: constrained harmonic and anharmonic analyses of macromolecules based on elastic network models. PMID:16845072
The ARTS web server for aligning RNA tertiary structures. PMID:16845038
ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins. PMID:16845026
DILIMOT: discovery of linear motifs in proteins. PMID:16845024
Protemot: prediction of protein binding sites with automatically extracted geometrical templates. PMID:16845015
oGNM: online computation of structural dynamics using the Gaussian Network Model. PMID:16845002
CUPSAT: prediction of protein stability upon point mutations. PMID:16845001
HARMONY: a server for the assessment of protein structures. PMID:16844999
sgTarget: a target selection resource for structural genomics. PMID:16844998
TarFisDock: a web server for identifying drug targets with docking approach. PMID:16844997
PreBI: prediction of biological interfaces of proteins in crystals. PMID:16844993
PAST: fast structure-based searching in the PDB. PMID:16844992
SABBAC: online Structural Alphabet-based protein BackBone reconstruction from Alpha-Carbon trace. PMID:16844979
ReadOut: structure-based calculation of direct and indirect readout energies and specificities for protein-DNA recognition. PMID:16844974
CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues. PMID:16844972
A Brownian dynamics study of the interactions of the luminal domains of the cytochrome b6f complex with plastocyanin and cytochrome c6: the effects of the Rieske FeS protein on the interactions. PMID:16844750
Global topological features of cancer proteins in the human interactome. PMID:16844706
Wiggle-predicting functionally flexible regions from primary sequence. PMID:16839194
Tools for integrated sequence-structure analysis with UCSF Chimera. PMID:16836757
Processing multimode binding situations in simulation-based prediction of ligand-macromolecule affinities. PMID:16833982
Simple electrostatic model improves designed protein sequences. PMID:16823032
Markov propagation of allosteric effects in biomolecular systems: application to GroEL-GroES. PMID:16820777
Cloning, purification and crystallization of Bacillus anthracis class C acid phosphatase. PMID:16820700
Binding of adenine to Stx2, the protein toxin from Escherichia coli O157:H7. PMID:16820678
Mutagenic nucleotide incorporation and hindered translocation by a food carcinogen C8-dG adduct in Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4): modeling and dynamics studies. PMID:16820532
Information-driven protein-DNA docking using HADDOCK: it is a matter of flexibility. PMID:16820531
CYP153A6, a soluble P450 oxygenase catalyzing terminal-alkane hydroxylation. PMID:16816194
CIRSE: a solvation energy estimator compatible with flexible protein docking and design applications. PMID:16815913
Mitochondrial DNA sequence variation and mutation rate in patients with CADASIL. PMID:16807713
Novel knowledge-based mean force potential at the profile level. PMID:16803615
Identification of putative domain linkers by a neural network - application to a large sequence database. PMID:16800897
Electrostatic environment of hemes in proteins: pK(a)s of hydroxyl ligands. PMID:16800621
Probabilistic approach to determining unbiased random-coil carbon-13 chemical shift values from the protein chemical shift database. PMID:16799859
Molecular simulation of the binding of nerve growth factor peptide mimics to the receptor tyrosine kinase A. PMID:16798810
Unraveling the nature of the segmentation clock: Intrinsic disorder of clock proteins and their interaction map. PMID:16798096
Protein disorder prediction by condensed PSSM considering propensity for order or disorder. PMID:16796745
Quenchers induce wavelength dependence on protein fluorescence lifetimes. PMID:16794870
Theoretical modelling of tripodal CuN3 and CuN4 cuprous complexes interacting with O2, CO or CH3CN. PMID:16791643
The first crystal structure of class III superoxide reductase from Treponema pallidum. PMID:16791639
Reduction of dioxygen by enzymes containing copper. PMID:16791638
Prediction of RNA binding sites in proteins from amino acid sequence. PMID:16790841
Prediction of catalytic residues using Support Vector Machine with selected protein sequence and structural properties. PMID:16790052
Docking protein domains in contact space. PMID:16790041
Assessing the accuracy of ancestral protein reconstruction methods. PMID:16789817
Long-range cooperative binding effects in a T cell receptor variable domain. PMID:16788072
Comparison of a homology model and the crystallographic structure of human 11beta-hydroxysteroid dehydrogenase type 1 (11betaHSD1) in a structure-based identification of inhibitors. PMID:16783599
Computational prediction of homodimerization of the A3 adenosine receptor. PMID:16781879
A new measure for functional similarity of gene products based on Gene Ontology. PMID:16776819
Representation of target-bound drugs by computed conformers: implications for conformational libraries. PMID:16764718
Secondary structure spatial conformation footprint: a novel method for fast protein structure comparison and classification. PMID:16762072
ProFace: a server for the analysis of the physicochemical features of protein-protein interfaces. PMID:16759379
High throughput profile-profile based fold recognition for the entire human proteome. PMID:16759376
Neutralization epitope responsible for the hepatitis B virus subtype-specific protection in chimpanzees. PMID:16757558
The purification, crystallization and preliminary structural characterization of human MAWDBP, a member of the phenazine biosynthesis-like protein family. PMID:16754977
Testing for spatial clustering of amino acid replacements within protein tertiary structure. PMID:16752209
X-ray structure of potato epoxide hydrolase sheds light on substrate specificity in plant enzymes. PMID:16751602
Chromophore structure in the photocycle of the cyanobacterial phytochrome Cph1. PMID:16751241
Automated functional classification of experimental and predicted protein structures. PMID:16749925
EVEREST: automatic identification and classification of protein domains in all protein sequences. PMID:16749920
Crystal structure of neurotropism-associated variable surface protein 1 (Vsp1) of Borrelia turicatae. PMID:16740958
Polymorphism, natural selection, and structural modeling of class Ia MHC in the African clawed frog (Xenopus laevis). PMID:16738940
Protein complex compositions predicted by structural similarity. PMID:16738133
Characterization of Ca2+ interactions with matrix metallopeptidase-12: implications for matrix metallopeptidase regulation. PMID:16737445
Protein engineering of a cold-active beta-galactosidase from Arthrobacter sp. SB to increase lactose hydrolysis reveals new sites affecting low temperature activity. PMID:16736094
Intrinsic disorder in transcription factors. PMID:16734424
Positioning of proteins in membranes: a computational approach. PMID:16731967
Configurational entropy change of netropsin and distamycin upon DNA minor-groove binding. PMID:16731550
How azide inhibits ATP hydrolysis by the F-ATPases. PMID:16728506
Prediction of three dimensional structure of calmodulin. PMID:16721661
Soret spectral and bioinformatic approaches provide evidence for a critical role of the alpha -subunit in assembly of tetrameric hemoglobin. PMID:16721660
Predicting DNA-binding sites of proteins from amino acid sequence. PMID:16712732
Statistics of knots, geometry of conformations, and evolution of proteins. PMID:16710448
Locating active-site hydrogen atoms in D-xylose isomerase: time-of-flight neutron diffraction. PMID:16707576
A newly designed microspectrofluorometer for kinetic studies on protein crystals in combination with x-ray diffraction. PMID:16698776
From the similarity analysis of protein cavities to the functional classification of protein families using cavbase. PMID:16697007
A contact energy function considering residue hydrophobic environment and its application in protein fold recognition. PMID:16689689
Characterizing the microenvironment surrounding phosphorylated protein sites. PMID:16689688
Designing a nanotube using naturally occurring protein building blocks. PMID:16683021
Crystallization of recombinant Haemophilus influenzae e (P4) acid phosphatase. PMID:16682777
Automated extraction and classification of RNA tertiary structure cyclic motifs. PMID:16679452
Recurrent use of evolutionary importance for functional annotation of proteins based on local structural similarity. PMID:16672239
Evaluation of sequence alignments and oligonucleotide probes with respect to three-dimensional structure of ribosomal RNA using ARB software package. PMID:16672074
Electrostatics of ligand binding: parametrization of the generalized Born model and comparison with the Poisson-Boltzmann approach. PMID:16671749
Protein Alpha Shape (PAS) Dock: a new gaussian-based score function suitable for docking in homology modelled protein structures. PMID:16652207
On the accuracy of homology modeling and sequence alignment methods applied to membrane proteins. PMID:16648166
Stoichiometry of lipid interactions with transmembrane proteins--Deduced from the 3D structures. PMID:16641489
An algorithm for predicting protein-protein interaction sites: Abnormally exposed amino acid residues and secondary structure elements. PMID:16641487
Development of quantitative structure-binding affinity relationship models based on novel geometrical chemical descriptors of the protein-ligand interfaces. PMID:16640331
Conformational equilibrium of cytochrome P450 BM-3 complexed with N-palmitoylglycine: a replica exchange molecular dynamics study. PMID:16637647
Joint use of small-angle X-ray and neutron scattering to study biological macromolecules in solution. PMID:16636827
A computational protocol for the integration of the monotopic protein prostaglandin H2 synthase into a phospholipid bilayer. PMID:16632499
Conformational changes in protein loops and helices induced by post-translational phosphorylation. PMID:16628247
An analysis of the Sargasso Sea resource and the consequences for database composition. PMID:16623953
Fold-recognition and comparative modeling of human alpha2,3-sialyltransferases reveal their sequence and structural similarities to CstII from Campylobacter jejuni. PMID:16620397
Evolution of structural shape in bacterial globin-related proteins. PMID:16612536
Protein farnesyltransferase: flexible docking studies on inhibitors using computational modeling. PMID:16607571
Molecular properties of P2X receptors. PMID:16607539
A comparative study of available software for high-accuracy homology modeling: from sequence alignments to structural models. PMID:16600967
Local structure of beta-hairpin isotopomers by FTIR, 2D IR, and ab initio theory. PMID:16599536
Protein-lipid interactions: correlation of a predictive algorithm for lipid-binding sites with three-dimensional structural data. PMID:16569237
The inherent structure landscape of a protein. PMID:16567628
Structural proteomics of minimal organisms: conservation of protein fold usage and evolutionary implications. PMID:16566839
Evidence for a dynamic role for homocitrate during nitrogen fixation: the effect of substitution at the alpha-Lys426 position in MoFe-protein of Azotobacter vinelandii. PMID:16566750
Gaussian-weighted RMSD superposition of proteins: a structural comparison for flexible proteins and predicted protein structures. PMID:16565070
Amino acid size, charge, hydropathy indices and matrices for protein structure analysis. PMID:16551371
Application of a sensitive collection heuristic for very large protein families: evolutionary relationship between adipose triglyceride lipase (ATGL) and classic mammalian lipases. PMID:16551354
Exploring dynamics of protein structure determination and homology-based prediction to estimate the number of superfamilies and folds. PMID:16549009
A role for direct interactions in the modulation of rhodopsin by omega-3 polyunsaturated lipids. PMID:16547139
Free-energy force-field three-dimensional quantitative structure-activity relationship analysis of a set of p38-mitogen activated protein kinase inhibitors. PMID:16541250
Fitness cost of escape mutations in p24 Gag in association with control of human immunodeficiency virus type 1. PMID:16537629
Common mechanism of pore opening shared by five different potassium channels. PMID:16533848
A molecular dynamics study of the effect of Ca2+ removal on calmodulin structure. PMID:16533845
Identification of similar regions of protein structures using integrated sequence and structure analysis tools. PMID:16526955
Towards genome-scale structure prediction for transmembrane proteins. PMID:16524835
Fold classification based on secondary structure--how much is gained by including loop topology? PMID:16524467
Structural model of an antistasin/notch-like fusion protein from the cocoon wall of the aquatic leech, Theromyzon tessulatum. PMID:16523290
Structural and evolutionary classification of G/U wobble basepairs in the ribosome. PMID:16522645
Computational approaches for predicting the biological effect of p53 missense mutations: a comparison of three sequence analysis based methods. PMID:16522644
Expression, purification, crystallization and preliminary X-ray analysis of the human RuvB-like protein RuvBL1. PMID:16511264
Crystallization of a newly discovered histidine acid phosphatase from Francisella tularensis. PMID:16511256
Deposit3D: a tool for automating structure depositions to the Protein Data Bank. PMID:16511167
Crystallization and preliminary X-ray analysis of a truncated mutant of yeast nuclear thiol peroxidase, a novel atypical 2-Cys peroxiredoxin. PMID:16511121
Crystallization and preliminary X-ray crystallographic analysis of yeast NAD+-specific isocitrate dehydrogenase. PMID:16511075
Crystallization and preliminary X-ray analysis of Mlc from Escherichia coli. PMID:16510988
Structure of human factor VIIa/tissue factor in complex with a peptide-mimetic inhibitor: high selectivity against thrombin by introducing two charged groups in P2 and P4. PMID:16510984
Crystallization and preliminary X-ray diffraction analysis of a lectin from Canavalia maritima seeds. PMID:16508099
Ultrahigh resolution crystal structures of human carbonic anhydrases I and II complexed with "two-prong" inhibitors reveal the molecular basis of high affinity. PMID:16506782
An insight into the molecular basis of salt tolerance of L-myo-inositol 1-P synthase (PcINO1) from Porteresia coarctata (Roxb.) Tateoka, a halophytic wild rice. PMID:16500989
cAMP Modulation of the cytoplasmic domain in the HCN2 channel investigated by molecular simulations. PMID:16500960
Crystal structure of the murine cytomegalovirus MHC-I homolog m144. PMID:16500675
Coarse grained protein-lipid model with application to lipoprotein particles. PMID:16494423
Cyclo[n]pyrroles: size and site-specific binding to G-quadruplexes. PMID:16492050
Structure modeling of all identified G protein-coupled receptors in the human genome. PMID:16485037
The RNA Ontology Consortium: an open invitation to the RNA community. PMID:16484377
Prediction of protein continuum secondary structure with probabilistic models based on NMR solved structures. PMID:16478545
Crystal structures of two putative phosphoheptose isomerases. PMID:16477602
Conserved thermodynamic contributions of backbone hydrogen bonds in a protein fold. PMID:16473949
Immunophysical properties and prediction of activities for vaccinia virus complement control protein and smallpox inhibitor of complement enzymes using molecular dynamics and electrostatics. PMID:16473914
BALLView: an object-oriented molecular visualization and modeling framework. PMID:16470421
Crystal structure of obelin after Ca2+-triggered bioluminescence suggests neutral coelenteramide as the primary excited state. PMID:16467137
Characterization of the cysteine protease domain of Semliki Forest virus replicase protein nsP2 by in vitro mutagenesis. PMID:16466719
Traditional biomolecular structure determination by NMR spectroscopy allows for major errors. PMID:16462939
Gas phase characterization of the noncovalent quaternary structure of cholera toxin and the cholera toxin B subunit pentamer. PMID:16461395
Unfolding, aggregation, and amyloid formation by the tetramerization domain from mutant p53 associated with lung cancer. PMID:16460008
A new anti conformation for N-(deoxyguanosin-8-yl)-2-acetylaminofluorene (AAF-dG) allows Watson-Crick pairing in the Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4). PMID:16452300
A study on chirality in biomolecules: the effect of the exchange of L: amino acids to D: ones in Sso7d ribonuclease. PMID:16437209
Protein structure similarity from Principle Component Correlation analysis. PMID:16436213
Loop motions of triosephosphate isomerase observed with elastic networks. PMID:16430213
Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: recognition of pyrimidine-purine and purine-purine steps. PMID:16427082
Modeling the bound conformation of Pemphigus vulgaris-associated peptides to MHC Class II DR and DQ alleles. PMID:16426456
NOXclass: prediction of protein-protein interaction types. PMID:16423290
Defining the sequence-recognition profile of DNA-binding molecules. PMID:16418267
A theoretical model of Aquifex pyrophilus flagellin: implications for its thermostability. PMID:16411078
Serine/arginine-rich splicing factors belong to a class of intrinsically disordered proteins. PMID:16407336
Local protein structure prediction using discriminative models. PMID:16405736
Investigation of the binding mode of (-)-meptazinol and bis-meptazinol derivatives on acetylcholinesterase using a molecular docking method. PMID:16404617
Study on improving the selectivity of compounds that inhibit two PI3Ks (gamma and delta). PMID:16404616
SuperMimic--fitting peptide mimetics into protein structures. PMID:16403211
Cluster analysis of networks generated through homology: automatic identification of important protein communities involved in cancer metastasis. PMID:16398927
Escherichia coli K-12: a cooperatively developed annotation snapshot--2005. PMID:16397293
FAMCS: finding all maximal common substructures in proteins. PMID:16393147
Mutational spectrum of D-bifunctional protein deficiency and structure-based genotype-phenotype analysis. PMID:16385454
Epitome: database of structure-inferred antigenic epitopes. PMID:16381978
DBD: a transcription factor prediction database. PMID:16381970
pSTIING: a 'systems' approach towards integrating signalling pathways, interaction and transcriptional regulatory networks in inflammation and cancer. PMID:16381926
AffinDB: a freely accessible database of affinities for protein-ligand complexes from the PDB. PMID:16381925
MetaCyc: a multiorganism database of metabolic pathways and enzymes. PMID:16381923
SGCEdb: a flexible database and web interface integrating experimental results and analysis for structural genomics focusing on Caenorhabditis elegans. PMID:16381914
PUMA2--grid-based high-throughput analysis of genomes and metabolic pathways. PMID:16381888
INVHOGEN: a database of homologous invertebrate genes. PMID:16381884
The SWISS-MODEL Repository: new features and functionalities. PMID:16381875
SCOPPI: a structural classification of protein-protein interfaces. PMID:16381874
The RCSB PDB information portal for structural genomics. PMID:16381872
The Database of Macromolecular Motions: new features added at the decade mark. PMID:16381870
iMOTdb--a comprehensive collection of spatially interacting motifs in proteins. PMID:16381866
Flexible Structural Neighborhood--a database of protein structural similarities and alignments. PMID:16381864
SitesBase: a database for structure-based protein-ligand binding site comparisons. PMID:16381853
ProTherm and ProNIT: thermodynamic databases for proteins and protein-nucleic acid interactions. PMID:16381846
PPD v1.0--an integrated, web-accessible database of experimentally determined protein pKa values. PMID:16381845
PINT: Protein-protein Interactions Thermodynamic Database. PMID:16381844
MeRNA: a database of metal ion binding sites in RNA structures. PMID:16381830
IRESite: the database of experimentally verified IRES structures (www.iresite.org). PMID:16381829
The evolutionary history of Cys-tRNACys formation. PMID:16380427
The effect of a tightly bound water molecule on scaffold diversity in the computer-aided de novo ligand design of CDK2 inhibitors. PMID:16374623
Multipass membrane protein structure prediction using Rosetta. PMID:16372357
Prediction of beta-strand packing interactions using the signature product. PMID:16365772
Use of urea and glycine betaine to quantify coupled folding and probe the burial of DNA phosphates in lac repressor-lac operator binding. PMID:16363803
Molecular pathology of X linked retinoschisis: mutations interfere with retinoschisin secretion and oligomerisation. PMID:16361673
Lectin receptor kinases participate in protein-protein interactions to mediate plasma membrane-cell wall adhesions in Arabidopsis. PMID:16361528
Fatty acid binding proteins: same structure but different binding mechanisms? Molecular dynamics simulations of intestinal fatty acid binding protein. PMID:16361342
Can conformational change be described by only a few normal modes? PMID:16361336
MachineProse: an ontological framework for scientific assertions. PMID:16357355
Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state. PMID:16354836
A hybrid genetic-neural system for predicting protein secondary structure. PMID:16351752
Modeling study of the influences of the aromatic transitions and the local environment on the far-UV rotational strengths in TEM-1 beta-lactamase. PMID:16344949
The environment of amide groups in protein-ligand complexes: H-bonds and beyond. PMID:16344948
Potential of mean force calculation for the proton and hydride transfer reactions catalyzed by medium-chain acyl-CoA dehydrogenase: effect of mutations on enzyme catalysis. PMID:16342946
Effects of protein-pheromone complexation on correlated chemical shift modulations. PMID:16341752
Molecular docking study on the "back door" hypothesis for product clearance in acetylcholinesterase. PMID:16341717
Oligomeric protein structure networks: insights into protein-protein interactions. PMID:16336694
Biochemical characterization of the recombinant human Drosophila homologues Timekeeper and Andante involved in the Drosophila circadian oscillator. PMID:16335535
Primary and secondary interactions between CK2alpha and CK2beta lead to ring-like structures in the crystals of the CK2 holoenzyme. PMID:16335523
Glycolytic enzyme interactions with yeast and skeletal muscle F-actin. PMID:16326908
A common dimerization interface in bacterial response regulators KdpE and TorR. PMID:16322582
DSD--an integrated, web-accessible database of Dehydrogenase Enzyme Stereospecificities. PMID:16318635
The distance-profile representation and its application to detection of distantly related protein families. PMID:16316461
The Membrane Protein Data Bank. PMID:16314922
Effect of hsp70 chaperone on the folding and misfolding of polypeptides modeling an elongating protein chain. PMID:16309705
Validated ligand mapping of ACE active site. PMID:16307311
Reconstitution of cyanogenesis in barley (Hordeum vulgare L.) and its implications for resistance against the barley powdery mildew fungus. PMID:16307283
AntiJen: a quantitative immunology database integrating functional, thermodynamic, kinetic, biophysical, and cellular data. PMID:16305757
An ontology for immune epitopes: application to the design of a broad scope database of immune reactivities. PMID:16305755
IMGT, the international ImMunoGeneTics information system: a standardized approach for immunogenetics and immunoinformatics. PMID:16305737
Structural plasticity of the cyclic-cystine-knot framework: implications for biological activity and drug design. PMID:16300479
Identification of amino acids in HIV-1 and avian sarcoma virus integrase subsites required for specific recognition of the long terminal repeat Ends. PMID:16298997
The structure of the GPIb-filamin A complex. PMID:16293600
Spectral properties of contact matrix: application to proteins. PMID:16292476
From DNA to fitness differences: sequences and structures of adaptive variants of Colias phosphoglucose isomerase (PGI). PMID:16292000
ENPDA: an evolutionary structure-based de novo peptide design algorithm. PMID:16267689
Divergent evolution within protein superfolds inferred from profile-based phylogenetics. PMID:16266719
Modulation of oxygen binding to insect hemoglobins: the structure of hemoglobin from the botfly Gasterophilus intestinalis. PMID:16260762
Solution structure of (gamma)S-crystallin by molecular fragment replacement NMR. PMID:16260758
A novel approach to structural alignment using realistic structural and environmental information. PMID:16260755
KDE Bioscience: platform for bioinformatics analysis workflows. PMID:16260186
Estimating the accuracy of protein structures using residual dipolar couplings. PMID:16258827
An information theoretic approach to macromolecular modeling: II. Force fields. PMID:16254390
Analysis of binding sites for the new small-molecule CCR5 antagonist TAK-220 on human CCR5. PMID:16251315
Building native protein conformation from highly approximate backbone torsion angles. PMID:16251268
Structural characterization of proteins using residue environments. PMID:16245324
Structural evolution of the protein kinase-like superfamily. PMID:16244704
A Brownian dynamics study of the effects of cytochrome f structure and deletion of its small domain in interactions with cytochrome c6 and plastocyanin in Chlamydomonas reinhardtii. PMID:16239335
Structure and increased thermostability of Rhodococcus sp. naphthalene 1,2-dioxygenase. PMID:16237006
Specific translocation of protein kinase Calpha to the plasma membrane requires both Ca2+ and PIP2 recognition by its C2 domain. PMID:16236797
Modeling the signaling endosome hypothesis: why a drive to the nucleus is better than a (random) walk. PMID:16236165
The copper-iron connection in biology: structure of the metallo-oxidase Fet3p. PMID:16230618
Fibrinogen substrate recognition by staphylocoagulase.(pro)thrombin complexes. PMID:16230339
The quantitative relationship between structure and polarized spectroscopy in the FMO complex of Prosthecochloris aestuarii: refining experiments and simulations. PMID:16228505
The modeled structure of the RNA dependent RNA polymerase of GBV-C virus suggests a role for motif E in Flaviviridae RNA polymerases. PMID:16225688
Prediction of beta-barrel membrane proteins by searching for restricted domains. PMID:16225682
Conservation and relative importance of residues across protein-protein interfaces. PMID:16221766
An inquiry into protein structure and genetic disease: introducing undergraduates to bioinformatics in a large introductory course. PMID:16220142
A Brownian dynamics study of the interaction of Phormidium cytochrome f with various cyanobacterial plastocyanins. PMID:16214856
Protein production and crystallization at SECSG -- an overview. PMID:16211524
High-throughput protein production for X-ray crystallography and use of size exclusion chromatography to validate or refute computational biological unit predictions. PMID:16211510
Interpreting dynamically-averaged scalar couplings in proteins. PMID:16211481
Inferring protein domain interactions from databases of interacting proteins. PMID:16207360
Adding some SPICE to DAS. PMID:16204122
Crystal structure of the Yersinia type III secretion protein YscE. PMID:16195558
Mode of action and biochemical characterization of REP8839, a novel inhibitor of methionyl-tRNA synthetase. PMID:16189106
MACiE: a database of enzyme reaction mechanisms. PMID:16188925
Implementation of smooth continuous camera trajectories for viewing PDB and VRML objects. PMID:16184432
Transmembrane glycine zippers: physiological and pathological roles in membrane proteins. PMID:16179394
Insights into the quaternary association of proteins through structure graphs: a case study of lectins. PMID:16173917
Protein secondary structure assignment revisited: a detailed analysis of different assignment methods. PMID:16164759
Association of cytochrome P450 enzymes is a determining factor in their catalytic activity. PMID:16163453
In-silico screening using flexible ligand binding pockets: a molecular dynamics-based approach. PMID:16163449
Engineering stable peptide toxins by means of backbone cyclization: stabilization of the alpha-conotoxin MII. PMID:16162671
Prediction of protein thermostability with a direction- and distance-dependent knowledge-based potential. PMID:16155198
Cumulative effect of amino acid replacements results in enhanced thermostability of potato type L alpha-glucan phosphorylase. PMID:16151135
A network representation of protein structures: implications for protein stability. PMID:16150969
GASH: an improved algorithm for maximizing the number of equivalent residues between two protein structures. PMID:16146579
Nucleic acid chaperons: a theory of an RNA-assisted protein folding. PMID:16137324
A crystallographic study of Cys69Ala flavodoxin II from Azotobacter vinelandii: structural determinants of redox potential. PMID:16131657
Molecular basis for increased susceptibility of isolates with atazanavir resistance-conferring substitution I50L to other protease inhibitors. PMID:16127059
A protein domain interaction interface database: InterPare. PMID:16122378
Genomes are covered with ubiquitous 11 bp periodic patterns, the "class A flexible patterns". PMID:16120222
A combination of docking, QM/MM methods, and MD simulation for binding affinity estimation of metalloprotein ligands. PMID:16107143
Interaction preferences across protein-protein interfaces of obligatory and non-obligatory components are different. PMID:16105176
The Ramachandran plots of glycine and pre-proline. PMID:16105172
A fold-recognition approach to loop modeling. PMID:16096805
PALSSE: a program to delineate linear secondary structural elements from protein structures. PMID:16095538
Atomic resolution structures of resting-state, substrate- and product-complexed Cu-nitrite reductase provide insight into catalytic mechanism. PMID:16093314
Prediction of inter-residue contacts map based on genetic algorithm optimized radial basis function neural network and binary input encoding scheme. PMID:16075311
Model of full-length HIV-1 integrase complexed with viral DNA as template for anti-HIV drug design. PMID:16075307
Early-stage folding in proteins (in silico) sequence-to-structure relation. PMID:16046811
Disabling TNF receptor signaling by induced conformational perturbation of tryptophan-107. PMID:16043718
Structure, function, and evolution of transient and obligate protein-protein interactions. PMID:16043700
BioMagResBank databases DOCR and FRED containing converted and filtered sets of experimental NMR restraints and coordinates from over 500 protein PDB structures. PMID:16041478
Effective function annotation through catalytic residue conservation. PMID:16037208
Functional analysis of the glycero-manno-heptose 7-phosphate kinase domain from the bifunctional HldE protein, which is involved in ADP-L-glycero-D-manno-heptose biosynthesis. PMID:16030223
Design of cyclic and other templates for potent and selective peptide alpha-MSH analogues. PMID:16023401
The solution structure of the Josephin domain of ataxin-3: structural determinants for molecular recognition. PMID:16020535
X-ray reflectivity studies of cPLA2{alpha}-C2 domains adsorbed onto Langmuir monolayers of SOPC. PMID:15994899
PRISM: protein interactions by structural matching. PMID:15991339
Rv0216, a conserved hypothetical protein from Mycobacterium tuberculosis that is essential for bacterial survival during infection, has a double hotdog fold. PMID:15987908
The effect of long-range interactions on the secondary structure formation of proteins. PMID:15987894
The E. coli NusA carboxy-terminal domains are structurally similar and show specific RNAP- and lambdaN interaction. PMID:15987884
An inactivated nuclease-like domain in RecC with novel function: implications for evolution. PMID:15985153
A robust bulk-solvent correction and anisotropic scaling procedure. PMID:15983406
PISCES: recent improvements to a PDB sequence culling server. PMID:15980589
ProFunc: a server for predicting protein function from 3D structure. PMID:15980588
Fragment Finder: a web-based software to identify similar three-dimensional structural motif. PMID:15980587
MRS: a fast and compact retrieval system for biological data. PMID:15980580
Recent additions and improvements to the Onto-Tools. PMID:15980579
SCRATCH: a protein structure and structural feature prediction server. PMID:15980571
AISMIG--an interactive server-side molecule image generator. PMID:15980568
BASys: a web server for automated bacterial genome annotation. PMID:15980511
RPBS: a web resource for structural bioinformatics. PMID:15980507
SPACE: a suite of tools for protein structure prediction and analysis based on complementarity and environment. PMID:15980496
PCE: web tools to compute protein continuum electrostatics. PMID:15980492
PPG: online generation of protein pictures and animations. PMID:15980481
SRide: a server for identifying stabilizing residues in proteins. PMID:15980477
ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures. PMID:15980475
FFAS03: a server for profile--profile sequence alignments. PMID:15980471
SCANMOT: searching for similar sequences using a simultaneous scan of multiple sequence motifs. PMID:15980468
SOAP-based services provided by the European Bioinformatics Institute. PMID:15980463
SEARCHGTr: a program for analysis of glycosyltransferases involved in glycosylation of secondary metabolites. PMID:15980457
TMBETA-NET: discrimination and prediction of membrane spanning beta-strands in outer membrane proteins. PMID:15980447
AS2TS system for protein structure modeling and analysis. PMID:15980437
Effects of urea and trimethylamine-N-oxide (TMAO) on the interactions of lysozyme in solution. PMID:15980169
A molecular docking model of SARS-CoV S1 protein in complex with its receptor, human ACE2. PMID:15979045
A test of enhancing model accuracy in high-throughput crystallography. PMID:15965733
Comparative 3-D modeling of tmRNA. PMID:15958166
The multiple personalities of the regulatory subunit of protein kinase CK2: CK2 dependent and CK2 independent roles reveal a secret identity for CK2beta. PMID:15951851
The exchangeability of amino acids in proteins. PMID:15944362
SuperLigands - a database of ligand structures derived from the Protein Data Bank. PMID:15943884
Coupling between catalytic site and collective dynamics: a requirement for mechanochemical activity of enzymes. PMID:15939021
Do all backbone polar groups in proteins form hydrogen bonds? PMID:15937286
Do all backbone polar groups in proteins form hydrogen bonds? PMID:15937286
Crystal structure of the "PhoU-like" phosphate uptake regulator from Aquifex aeolicus. PMID:15937186
Crystal structure of the protease-resistant core domain of Yersinia pestis virulence factor YopR. PMID:15930010
High-quality homology models derived from NMR and X-ray structures of E. coli proteins YgdK and Suf E suggest that all members of the YgdK/Suf E protein family are enhancers of cysteine desulfurases. PMID:15930006
Structural model of the amino propeptide of collagen XI alpha1 chain with similarity to the LNS domains. PMID:15930001
Structural and functional characterization of CFE88: evidence that a conserved and essential bacterial protein is a methyltransferase. PMID:15929997
Aminoacylation and conformational properties of yeast mitochondrial tRNA mutants with respiratory deficiency. PMID:15923375
Global rigid body modeling of macromolecular complexes against small-angle scattering data. PMID:15923225
Structural basis of chaperone-subunit complex recognition by the type 1 pilus assembly platform FimD. PMID:15920478
Theoretical model of prion propagation: a misfolded protein induces misfolding. PMID:15911770
The rate of compensatory mutation in the DNA bacteriophage phiX174. PMID:15911582
The design and implementation of the immune epitope database and analysis resource. PMID:15895191
Role of intramolecular vibrations in long-range electron transfer between pheophytin and ubiquinone in bacterial photosynthetic reaction centers. PMID:15894646
Molecular dynamics of a protein surface: ion-residues interactions. PMID:15894639
Physics-based protein-structure prediction using a hierarchical protocol based on the UNRES force field: assessment in two blind tests. PMID:15894609
On the orientation of the backbone dipoles in native folds. PMID:15894608
Structural and functional characterization of AtPTR3, a stress-induced peptide transporter of Arabidopsis. PMID:15889294
A hypothesis for GPCR activation. PMID:15889287
Common patterns in type II restriction enzyme binding sites. PMID:15888729
Tertiary windowing to detect positive diversifying selection. PMID:15883884
Phylogenetic differences in content and intensity of periodic proteins. PMID:15883880
Domain swapping in the low-similarity isomerase/hydratase superfamily: the crystal structure of rat mitochondrial Delta3, Delta2-enoyl-CoA isomerase. PMID:15883186
Structural and functional dissection of the Abp1 ADFH actin-binding domain reveals versatile in vivo adapter functions. PMID:15872087
Crystal structure of levansucrase from the Gram-negative bacterium Gluconacetobacter diazotrophicus. PMID:15869470
Electrostatics of Cytochrome-c assemblies. PMID:15868153
Exploring relationships and mining data with the UCSC Gene Sorter. PMID:15867434
iGNM: a database of protein functional motions based on Gaussian Network Model. PMID:15860562
Detailed protein sequence alignment based on Spectral Similarity Score (SSS). PMID:15850477
Unsupervised guided docking of covalently bound ligands. PMID:15849994
TM-align: a protein structure alignment algorithm based on the TM-score. PMID:15849316
Computational studies on imidazole heme conformations. PMID:15843984
Cloning, characterization and structural model of a FatA-type thioesterase from sunflower seeds (Helianthus annuus L.). PMID:15841386
Crystal structures of apo wild-type M. jannaschii tyrosyl-tRNA synthetase (TyrRS) and an engineered TyrRS specific for O-methyl-L-tyrosine. PMID:15840835
Rigid-cluster models of conformational transitions in macromolecular machines and assemblies. PMID:15833998
Filtering high-throughput protein-protein interaction data using a combination of genomic features. PMID:15833142
Asymmetry in RNA pseudoknots: observation and theory. PMID:15831794
Detecting DNA-binding helix-turn-helix structural motifs using sequence and structure information. PMID:15831786
Dimanganese catalase--spectroscopic parameters from broken-symmetry density functional theory of the superoxidized Mn(III)/Mn(IV) state. PMID:15830216
Functional dynamics of PDZ binding domains: a normal-mode analysis. PMID:15821164
Regulation of ecdysteroid signalling during Drosophila development: identification, characterization and modelling of ecdysone oxidase, an enzyme involved in control of ligand concentration. PMID:15813704
Super paramagnetic clustering of protein sequences. PMID:15804359
Statistically significant dependence of the Xaa-Pro peptide bond conformation on secondary structure and amino acid sequence. PMID:15804350
Visualization of conformational distribution of short to medium size segments in globular proteins and identification of local structural motifs. PMID:15802651
Improved side-chain modeling for protein-protein docking. PMID:15802647
Columba: an integrated database of proteins, structures, and annotations. PMID:15801979
A comparison of the binding sites of matrix metalloproteinases and tumor necrosis factor-alpha converting enzyme: implications for selectivity. PMID:15801829
Identification of key amino acids responsible for the substantially higher affinities of human type 1 3beta-hydroxysteroid dehydrogenase/isomerase (3beta-HSD1) for substrates, coenzymes, and inhibitors relative to human 3beta-HSD2. PMID:15797861
A novel GCAP1 missense mutation (L151F) in a large family with autosomal dominant cone-rod dystrophy (adCORD). PMID:15790869
Comparative mapping of sequence-based and structure-based protein domains. PMID:15790427
Tyrosine phosphorylation of myosin heavy chain during skeletal muscle differentiation: an integrated bioinformatics approach. PMID:15790426
A low-molecular-weight compound discovered through virtual database screening inhibits Stat3 function in breast cancer cells. PMID:15781862
Chicken genome analysis reveals novel genes encoding biotin-binding proteins related to avidin family. PMID:15777476
Accommodation of a 1S-(-)-benzo[c]phenanthrenyl-N6-dA adduct in the Y-family Dpo4 DNA polymerase active site: structural insights through molecular dynamics simulations. PMID:15777084
Side-chain flexibility in protein-ligand binding: the minimal rotation hypothesis. PMID:15772311
Evolution of distinct EGF domains with specific functions. PMID:15772310
The flexibility in the proline ring couples to the protein backbone. PMID:15772308
BioAfrica's HIV-1 proteomics resource: combining protein data with bioinformatics tools. PMID:15757512
Asparagine and glutamine side-chain conformation in solution and crystal: a comparison for hen egg-white lysozyme using residual dipolar couplings. PMID:15754058
Variable selection and model validation of 2D and 3D molecular descriptors. PMID:15729846
Recognition of the spliceosomal branch site RNA helix on the basis of surface and electrostatic features. PMID:15728744
The intrinsic axial ligand effect on propene oxidation by horseradish peroxidase versus cytochrome P450 enzymes. PMID:15723206
Structure-function analysis of cf-9, a receptor-like protein with extracytoplasmic leucine-rich repeats. PMID:15722474
Spectral signal-to-noise ratio and resolution assessment of 3D reconstructions. PMID:15721578
PSSM-based prediction of DNA binding sites in proteins. PMID:15720719
Calpha-H...O = C hydrogen bonds contribute to the specificity of RGD cell-adhesion interactions. PMID:15710040
Backbone solution structures of proteins using residual dipolar couplings: application to a novel structural genomics target. PMID:15704012
Crystal structure of the hypothetical protein TA1238 from Thermoplasma acidophilum: a new type of helical super-bundle. PMID:15704011
Electrostatic modeling predicts the activities of orthopoxvirus complement control proteins. PMID:15699145
The Molecular Biology Toolkit (MBT): a modular platform for developing molecular visualization applications. PMID:15694009
Molecular adaptation in the ice worm, Mesenchytraeus solifugus: divergence of energetic-associated genes. PMID:15693622
Availability of short amino acid sequences in proteins. PMID:15689510
Identification of the ligand binding sites on the molecular surface of proteins. PMID:15689509
CGH2466, a combined adenosine receptor antagonist, p38 mitogen-activated protein kinase and phosphodiesterase type 4 inhibitor with potent in vitro and in vivo anti-inflammatory activities. PMID:15685201
Fluctuations and correlations in crystalline protein dynamics: a simulation analysis of staphylococcal nuclease. PMID:15681654
Experimental and simulative dissociation of dimeric Cu,Zn superoxide dismutase doubly mutated at the intersubunit surface. PMID:15681652
An evaluation of chemical shift index-based secondary structure determination in proteins: influence of random coil chemical shifts. PMID:15666561
Molecular dynamics simulations indicate a possible role of parallel beta-helices in seeded aggregation of poly-Gln. PMID:15665127
BODIL: a molecular modeling environment for structure-function analysis and drug design. PMID:15663001
Intramolecular disulphide bond arrangements in nonhomologous proteins. PMID:15659377
The N-terminal to C-terminal motif in protein folding and function. PMID:15657118
The protein structure prediction problem could be solved using the current PDB library. PMID:15653774
Crystal structures of RsbQ, a stress-response regulator in Bacillus subtilis. PMID:15632289
Phylogeny determined by protein domain content. PMID:15630082
Structure prediction of membrane proteins. PMID:15629037
Brownian dynamics study of cytochrome f interactions with cytochrome c6 and plastocyanin in Chlamydomonas reinhardtii plastocyanin, and cytochrome c6 mutants. PMID:15626695
The cAMP binding domain: an ancient signaling module. PMID:15618393
Kinetic isotope effects and ligand binding in PQQ-dependent methanol dehydrogenase. PMID:15617516
A surface loop of the potato leafroll virus coat protein is involved in virion assembly, systemic movement, and aphid transmission. PMID:15613347
The identification of novel RNA structural motifs using COMPADRES: an automated approach to structural discovery. PMID:15608296
IMGT, the international ImMunoGeneTics information system. PMID:15608269
The Adaptive Evolution Database (TAED): a phylogeny based tool for comparative genomics. PMID:15608245
The UCSC Proteome Browser. PMID:15608236
EzCatDB: the Enzyme Catalytic-mechanism Database. PMID:15608227
The Yeast Resource Center Public Data Repository. PMID:15608220
PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank. PMID:15608195
STING Report: convenient web-based application for graphic and tabular presentations of protein sequence, structure and function descriptors from the STING database. PMID:15608194
PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids. PMID:15608193
The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis. PMID:15608188
Carbohydrate Structure Suite (CSS): analysis of carbohydrate 3D structures derived from the PDB. PMID:15608187
PDB-Ligand: a ligand database based on PDB for the automated and customized classification of ligand-binding structures. PMID:15608186
STING Report: convenient web-based application for graphic and tabular presentations of protein sequence, structure and function descriptors from the STING database. PMID:15608194
PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids. PMID:15608193
The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis. PMID:15608188
Carbohydrate Structure Suite (CSS): analysis of carbohydrate 3D structures derived from the PDB. PMID:15608187
PDB-Ligand: a ligand database based on PDB for the automated and customized classification of ligand-binding structures. PMID:15608186
The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema. PMID:15608185
The SYSTERS Protein Family Database in 2005. PMID:15608183
The ProDom database of protein domain families: more emphasis on 3D. PMID:15608179
ADDA: a domain database with global coverage of the protein universe. PMID:15608174
Functional analyses of the chitin-binding domains and the catalytic domain of Brassica juncea chitinase BjCHI1. PMID:15604744
4SCOPmap: automated assignment of protein structures to evolutionary superfamilies. PMID:15598351
Structure and dynamics of Candida rugosa lipase: the role of organic solvent. PMID:15597204
Modeling the E. coli 4-hydroxybenzoic acid oligoprenyltransferase ( ubiA transferase) and characterization of potential active sites. PMID:15597200
Relaxation kinetics and the glassiness of native proteins: coupling of timescales. PMID:15596500
Molecular modeling of nearly full-length ErbB2 receptor. PMID:15596490
Interaction of three-finger toxins with phospholipid membranes: comparison of S- and P-type cytotoxins. PMID:15584897
Use of herpes simplex virus and pseudorabies virus chimeric glycoprotein D molecules to identify regions critical for membrane fusion. PMID:15583135
In silico study of amyloid beta-protein folding and oligomerization. PMID:15583128
Electric charge balance mechanism of extended soluble proteins. PMID:15576568
A novel method reveals that solvent water favors polyproline II over beta-strand conformation in peptides and unfolded proteins: conditional hydrophobic accessible surface area (CHASA). PMID:15576559
PreSPI: a domain combination based prediction system for protein-protein interaction. PMID:15576357
EFICAz: a comprehensive approach for accurate genome-scale enzyme function inference. PMID:15576349
Constraint Logic Programming approach to protein structure prediction. PMID:15571634
Inhibition of parainfluenza virus type 3 and Newcastle disease virus hemagglutinin-neuraminidase receptor binding: effect of receptor avidity and steric hindrance at the inhibitor binding sites. PMID:15564499
Molecular modelling prediction of ligand binding site flexibility. PMID:15562988
Random mutagenesis of the gene encoding a viral ligand for multiple cell entry receptors to obtain viral mutants altered for receptor usage. PMID:15557552
Comparative computational analysis of prion proteins reveals two fragments with unusual structural properties and a pattern of increase in hydrophobicity associated with disease-promoting mutations. PMID:15557265
Molecular modeling of family GH16 glycoside hydrolases: potential roles for xyloglucan transglucosylases/hydrolases in cell wall modification in the poaceae. PMID:15557263
A model of the acid sphingomyelinase phosphoesterase domain based on its remote structural homolog purple acid phosphatase. PMID:15557261
Prediction of quaternary assembly of SARS coronavirus peplomer. PMID:15555555
Protein engineering and applications of Candida rugosa lipase isoforms. PMID:15554150
Structure and function of the phenazine biosynthetic protein PhzF from Pseudomonas fluorescens. PMID:15545603
Folding Trp-cage to NMR resolution native structure using a coarse-grained protein model. PMID:15533926
In silico evidence for DNA polymerase-beta's substrate-induced conformational change. PMID:15507687
Implications for domain fusion protein-protein interactions based on structural information. PMID:15504241
The structurally constrained protein evolution model accounts for sequence patterns of the LbetaH superfamily. PMID:15500694
Evolutionarily conserved regions and hydrophobic contacts at the superfamily level: The case of the fold-type I, pyridoxal-5'-phosphate-dependent enzymes. PMID:15498941
PASBio: predicate-argument structures for event extraction in molecular biology. PMID:15494078
High-throughput computational and experimental techniques in structural genomics. PMID:15489337
High-throughput expression of C. elegans proteins. PMID:15489332
Interdomain tilt angle determines integrin-dependent function of the ninth and tenth FIII domains of human fibronectin. PMID:15485890
Calcium-induced tertiary structure modifications of endo-beta-1,3-glucanase from Pyrococcus furiosus in 7.9 M guanidinium chloride. PMID:15482259
Crystal structures of Escherichia coli ATP-dependent glucokinase and its complex with glucose. PMID:15466045
Helical packing patterns in membrane and soluble proteins. PMID:15465852
Automated prediction of protein function and detection of functional sites from structure. PMID:15456910
Atomic model of the Thermus thermophilus 70S ribosome developed in silico. PMID:15454463
Tertiary structure predictions on a comprehensive benchmark of medium to large size proteins. PMID:15454459
Ion permeation through the alpha-hemolysin channel: theoretical studies based on Brownian dynamics and Poisson-Nernst-Plank electrodiffusion theory. PMID:15454431
How does averaging affect protein structure comparison on the ensemble level? PMID:15454426
Average protein density is a molecular-weight-dependent function. PMID:15388866
Improved pKa calculations through flexibility based sampling of a water-dominated interaction scheme. PMID:15388865
In silico protein design by combinatorial assembly of protein building blocks. PMID:15388863
Computational protein design is a challenge for implicit solvation models. PMID:15377512
Reconstruction of ancestral protein sequences and its applications. PMID:15377393
PEDRo: a database for storing, searching and disseminating experimental proteomics data. PMID:15377392
Crystal structure of Bacillus subtilis YckF: structural and functional evolution. PMID:15363790
"Teaching old drugs to kill new bugs": structure-based discovery of anti-SARS drugs. PMID:15358186
Identifying DNA-binding proteins using structural motifs and the electrostatic potential. PMID:15356290
Comparative structural modeling and inference of conserved protein classes in Drosophila seminal fluid. PMID:15345744
A Brownian dynamics study of the interaction of Phormidium laminosum plastocyanin with Phormidium laminosum cytochrome f. PMID:15345580
A catalog of human cDNA expression clones and its application to structural genomics. PMID:15345055
Prediction of pKa and redox properties in the thioredoxin superfamily. PMID:15340164
Calculation of cyclodextrin binding affinities: energy, entropy, and implications for drug design. PMID:15339804
A complementary bioinformatics approach to identify potential plant cell wall glycosyltransferase-encoding genes. PMID:15333752
Energetics of galactose- and glucose-aromatic amino acid interactions: implications for binding in galactose-specific proteins. PMID:15322288
MUSCLE: a multiple sequence alignment method with reduced time and space complexity. PMID:15318951
Reassessing random-coil statistics in unfolded proteins. PMID:15314216
Approximate protein structural alignment in polynomial time. PMID:15304646
Interaction of DNA with clusters of amino acids in proteins. PMID:15302912
STING Millennium Suite: integrated software for extensive analyses of 3d structures of proteins and their complexes. PMID:15301693
Delineation and analysis of the conceptual data model implied by the "IUPAC Recommendations for Biochemical Nomenclature". PMID:15295113
Comparison of a 3D-model of the classical alpha-scorpion toxin V from Leiurus quinquestriatus quinquestriatus with other scorpion toxins. PMID:15287698
Members of a new group of chitinase-like genes are expressed preferentially in cotton cells with secondary walls. PMID:15284492
Evaluation of the relative stability of liganded versus ligand-free protein conformations using Simplicial Neighborhood Analysis of Protein Packing (SNAPP) method. PMID:15281134
Cloning, functional expression and characterization of three Phanerochaete chrysosporium endo-1,4-beta-xylanases. PMID:15278289
Evolutionary constraints associated with functional specificity of the CMGC protein kinases MAPK, CDK, GSK, SRPK, DYRK, and CK2alpha. PMID:15273306
A classification of disulfide patterns and its relationship to protein structure and function. PMID:15273305
Mutations in herpes simplex virus glycoprotein D that prevent cell entry via nectins and alter cell tropism. PMID:15273289
Anchor residues in protein-protein interactions. PMID:15269345
The crystal structure of Escherichia coli MoaB suggests a probable role in molybdenum cofactor synthesis. PMID:15269205
Towards higher-throughput membrane protein production for structural genomics initiatives. PMID:15263855
Mining frequent patterns in protein structures: a study of protease families. PMID:15262784
C-Terminal 23 kDa polypeptide of soybean Gly m Bd 28 K is a potential allergen. PMID:15252733
Evidence for ditopic coordination of phosphate diesters to [Mg(15-crown-5)]2+. Implications for magnesium biocoordination chemistry. PMID:15241659
Sequence-based prediction of protein domains. PMID:15240828
Multiple folding pathways of the SH3 domain. PMID:15240485
Simulation of the interaction between ScyTx and small conductance calcium-activated potassium channel by docking and MM-PBSA. PMID:15240449
Best alpha-helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information. PMID:15215532
Structural alignment of proteins by a novel TOPOFIT method, as a superimposition of common volumes at a topomax point. PMID:15215530
Database searching by flexible protein structure alignment. PMID:15215527
Analysis of the "thermodynamic information content" of a Homo sapiens structural database reveals hierarchical thermodynamic organization. PMID:15215522
Determinants of quaternary association in legume lectins. PMID:15215518
BSDD: Biomolecules Segment Display Device--a web-based interactive display tool. PMID:15215468
MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes. PMID:15215462
ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement. PMID:15215461
CaspR: a web server for automated molecular replacement using homology modelling. PMID:15215460
JavaProtein Dossier: a novel web-based data visualization tool for comprehensive analysis of protein structure. PMID:15215458
FATCAT: a web server for flexible structure comparison and structure similarity searching. PMID:15215455
Detecting distant homology with Meta-BASIC. PMID:15215454
ProteinDBS: a real-time retrieval system for protein structure comparison. PMID:15215453
CHOP: parsing proteins into structural domains. PMID:15215452
pvSOAR: detecting similar surface patterns of pocket and void surfaces of amino acid residues on proteins. PMID:15215448
PDBSiteScan: a program for searching for active, binding and posttranslational modification sites in the 3D structures of proteins. PMID:15215447
FoldMiner and LOCK 2: protein structure comparison and motif discovery on the web. PMID:15215444
Wurst: a protein threading server with a structural scoring function, sequence profiles and optimized substitution matrices. PMID:15215443
PROSPECT-PSPP: an automatic computational pipeline for protein structure prediction. PMID:15215441
iMolTalk: an interactive, internet-based protein structure analysis server. PMID:15215439
SCit: web tools for protein side chain conformation analysis. PMID:15215438
GDAP: a web tool for genome-wide protein disulfide bond prediction. PMID:15215411
SDPMOD: an automated comparative modeling server for small disulfide-bonded proteins. PMID:15215410
CysView: protein classification based on cysteine pairing patterns. PMID:15215409
The PredictProtein server. PMID:15215403
Qgrid: clustering tool for detecting charged and hydrophobic regions in proteins. PMID:15215360
ClusPro: a fully automated algorithm for protein-protein docking. PMID:15215358
ProteMiner-SSM: a web server for efficient analysis of similar protein tertiary substructures. PMID:15215355
InterWeaver: interaction reports for discovering potential protein interaction partners with online evidence. PMID:15215354
Consensus alignment server for reliable comparative modeling with distant templates. PMID:15215349
Correlation times and adiabatic barriers for methyl rotation in SNase. PMID:15213436
Exact solutions for internuclear vectors and backbone dihedral angles from NH residual dipolar couplings in two media, and their application in a systematic search algorithm for determining protein backbone structure. PMID:15213422
Homology building as a means to define antigenic epitopes on dihydrofolate reductase (DHFR) from Plasmodium falciparum. PMID:15193156
Molecular mechanism of domain swapping in proteins: an analysis of slower motions. PMID:15189881
Highly organized but pliant active site of DNA polymerase beta: compensatory mechanisms in mutant enzymes revealed by dynamics simulations and energy analyses. PMID:15189842
An overview of the basic helix-loop-helix proteins. PMID:15186484
pdb-care (PDB carbohydrate residue check): a program to support annotation of complex carbohydrate structures in PDB files. PMID:15180909
Structural characterization of an intermolecular RNA-RNA interaction involved in the transcription regulation element of a bipartite plant virus. PMID:15155850
Mechanism of action at the molecular level of the antiviral drug 3(2H)-isoflavene against type 2 poliovirus. PMID:15155227
Impact of antibody framework residue VH-71 on the stability of a humanised anti-MUC1 scFv and derived immunoenzyme. PMID:15150594
Recognition of functional sites in protein structures. PMID:15147845
Predicting transmembrane beta-barrels in proteomes. PMID:15141026
Visualizing sequence similarity of protein families. PMID:15140831
Use of a structural alphabet for analysis of short loops connecting repetitive structures. PMID:15140270
Sequence-structure mapping errors in the PDB: OB-fold domains. PMID:15133161
Progress towards mapping the universe of protein folds. PMID:15128436
Automated structure prediction of weakly homologous proteins on a genomic scale. PMID:15126668
Molecular dynamics simulation of matrix metalloproteinase 2: fluctuations and time evolution of recognition pockets. PMID:15124932
A structure-activity relationship study of catechol-O-methyltransferase inhibitors combining molecular docking and 3D QSAR methods. PMID:15124929
Three-dimensional motifs from the SCOR, structural classification of RNA database: extruded strands, base triples, tetraloops and U-turns. PMID:15121895
ASAView: database and tool for solvent accessibility representation in proteins. PMID:15119964
The modeling of the structure of the cysteine-rich domain of metabotropic glutamate receptors. PMID:15116561
A hybrid clustering approach to recognition of protein families in 114 microbial genomes. PMID:15115543
Frequent occurrence of recognition site-like sequences in the restriction endonucleases. PMID:15113406
Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PMID:15103394
MolTalk--a programming library for protein structures and structure analysis. PMID:15096277
Probable epitopes: Relationships between myelin basic protein antigenic determinants and viral and bacterial proteins. PMID:15067168
Structural characterization of genomes by large scale sequence-structure threading. PMID:15061866
Alterations at the peptidyl transferase centre of the ribosome induced by the synergistic action of the streptogramins dalfopristin and quinupristin. PMID:15059283
Enzymatic digestion and mass spectrometry in the study of advanced glycation end products/peptides. PMID:15047055
HIV-1 protease molecular dynamics of a wild-type and of the V82F/I84V mutant: possible contributions to drug resistance and a potential new target site for drugs. PMID:15044738
A new, structurally nonredundant, diverse data set of protein-protein interfaces and its implications. PMID:15044734
Orientational potentials extracted from protein structures improve native fold recognition. PMID:15044723
Similar active sites in lysostaphins and D-Ala-D-Ala metallopeptidases. PMID:15044722
The cell-centered database: a database for multiscale structural and protein localization data from light and electron microscopy. PMID:15043222
Simulation of (125)I decay in a synthetic oligodeoxynucleotide with normal and distorted geometry and the role of radiation and non-radiation actions. PMID:15042380
3D QSAR studies on peroxisome proliferator-activated receptor gamma agonists using CoMFA and CoMSIA. PMID:15022104
Assignment of protein backbone resonances using connectivity, torsion angles and 13Calpha chemical shifts. PMID:15017135
Theoretical model of the three-dimensional structure of a sugar-binding protein from Pyrococcus horikoshii: structural analysis and sugar-binding simulations. PMID:15015939
An expectation/maximization nuclear vector replacement algorithm for automated NMR resonance assignments. PMID:15014227
Identification of a stretch of six divergent amino acids on the alpha5 helix of Galpha16 as a major determinant of the promiscuity and efficiency of receptor coupling. PMID:15005654
Uncharged P-selectin blockers. PMID:15001841
Local feature frequency profile: a method to measure structural similarity in proteins. PMID:14985506
Sensitivity and selectivity in protein structure comparison. PMID:14978311
Improved side-chain prediction accuracy using an ab initio potential energy function and a very large rotamer library. PMID:14978310
Rapid evolution in conformational space: a study of loop regions in a ubiquitous GTP binding domain. PMID:14978301
Identification and mapping of self-assembling protein domains encoded by the Escherichia coli K-12 genome by use of lambda repressor fusions. PMID:14973045
The nsp9 replicase protein of SARS-coronavirus, structure and functional insights. PMID:14962394
Genetic evidence for interaction between eta- and beta-tubulins. PMID:14871951
Molecular modeling of the mGluR1 metabotropic glutamate receptor transmembrane domain and construction of the model of its dimer. PMID:14870616
Functional prediction of a T-DNA tagged gene of Arabidopsis thaliana by in silico analysis. PMID:14767695
Steric restrictions in protein folding: an alpha-helix cannot be followed by a contiguous beta-strand. PMID:14767081
The Yersinia adhesin YadA collagen-binding domain structure is a novel left-handed parallel beta-roll. PMID:14765110
ACE2 X-ray structures reveal a large hinge-bending motion important for inhibitor binding and catalysis. PMID:14754895
Interhelical angle and distance preferences in globular proteins. PMID:14747345
Rotational-echo double-resonance NMR-restrained model of the ternary complex of 5-enolpyruvylshikimate-3-phosphate synthase. PMID:14739636
Myoglobin cavities provide interior ligand pathway. PMID:14739317
The role of interleukin-8 and its receptors in inflammatory lung disease: implications for therapy. PMID:14720072
Consensus structural models for the amino terminal domain of the retrovirus restriction gene Fv1 and the murine leukaemia virus capsid proteins. PMID:14715087
Inhibition and substrate recognition--a computational approach applied to HIV protease. PMID:14713189
Modeling of enzyme-substrate complexes for the metalloproteases MMP-3, ADAM-9 and ADAM-10. PMID:14713188
Domain mapping of the Rad51 paralog protein complexes. PMID:14704354
Representation, searching and discovery of patterns of bases in complex RNA structures. PMID:14703124
Automated docking of ligands to an artificial active site: augmenting crystallographic analysis with computer modeling. PMID:14703123
Structural characterization of siliceous spicules from marine sponges. PMID:14695297
Theoretical and experimental study of the D2194G mutation in the C2 domain of coagulation factor V. PMID:14695293
Small angle x-ray scattering from lipid-bound myelin basic protein in solution. PMID:14695288
An optimal structure-discriminative amino acid index for protein fold recognition. PMID:14695283
Small-world communication of residues and significance for protein dynamics. PMID:14695252
Active site modeling in copper azurin molecular dynamics simulations. PMID:14691672
FoldMiner: structural motif discovery using an improved superposition algorithm. PMID:14691242
On the analysis of membrane protein circular dichroism spectra. PMID:14691226
Protein flexibility and intrinsic disorder. PMID:14691223
APD: the Antimicrobial Peptide Database. PMID:14681488
The mouse Gene Expression Database (GXD): updates and enhancements. PMID:14681482
MitoProteome: mitochondrial protein sequence database and annotation system. PMID:14681458
MetaCyc: a multiorganism database of metabolic pathways and enzymes. PMID:14681452
BRENDA, the enzyme database: updates and major new developments. PMID:14681450
dictyBase: a new Dictyostelium discoideum genome database. PMID:14681427
FusionDB: a database for in-depth analysis of prokaryotic gene fusion events. PMID:14681411
TOPS: an enhanced database of protein structural topology. PMID:14681405
The SUPERFAMILY database in 2004: additions and improvements. PMID:14681402
The distribution and query systems of the RCSB Protein Data Bank. PMID:14681399
IMGT/3Dstructure-DB and IMGT/StructuralQuery, a database and a tool for immunoglobulin, T cell receptor and MHC structural data. PMID:14681396
HOMSTRAD: recent developments of the Homologous Protein Structure Alignment Database. PMID:14681395
The ASTRAL Compendium in 2004. PMID:14681391
SCOR: Structural Classification of RNA, version 2.0. PMID:14681389
The KNOTTIN website and database: a new information system dedicated to the knottin scaffold. PMID:14681383
EyeSite: a semi-automated database of protein families in the eye. PMID:14681381
THGS: a web-based database of Transmembrane Helices in Genome Sequences. PMID:14681375
ProTherm, version 4.0: thermodynamic database for proteins and mutants. PMID:14681373
A Bayesian molecular interaction library. PMID:14677639
Three-dimensional structures of the A, B, and C capsids of rhesus monkey rhadinovirus: insights into gammaherpesvirus capsid assembly, maturation, and DNA packaging. PMID:14645575
Binding of alpha-hydroxy-beta-amino acid inhibitors to methionine aminopeptidase. The performance of two types of scoring functions. PMID:14635729
Molecular model of the neural dopamine transporter. PMID:14635728
Comparative binding energy analysis of haloalkane dehalogenase substrates: modelling of enzyme-substrate complexes by molecular docking and quantum mechanical calculations. PMID:14635723
Characterization of four lectin-like receptor kinases expressed in roots of Medicago truncatula. Structure, location, regulation of expression, and potential role in the symbiosis with Sinorhizobium meliloti. PMID:14630957
LCN6, a novel human epididymal lipocalin. PMID:14617364
A model of tripeptidyl-peptidase I (CLN2), a ubiquitous and highly conserved member of the sedolisin family of serine-carboxyl peptidases. PMID:14609438
New role for leucyl aminopeptidase in glutathione turnover. PMID:14583094
Structural basis of the GM2 gangliosidosis B variant. PMID:14577003
Effect of external stresses on protein conformation: a computer modelling study. PMID:14574523
Multiple structural alignment by secondary structures: algorithm and applications. PMID:14573862
Self-assembly of single integral membrane proteins into soluble nanoscale phospholipid bilayers. PMID:14573860
Constraints on the conformation of the cytoplasmic face of dark-adapted and light-excited rhodopsin inferred from antirhodopsin antibody imprints. PMID:14573859
On the properties and sequence context of structurally ambivalent fragments in proteins. PMID:14573856
Engineering peroxidase activity in myoglobin: the haem cavity structure and peroxide activation in the T67R/S92D mutant and its derivative reconstituted with protohaemin-l-histidine. PMID:14563209
Analysis of sequence periodicity in E. coli proteins: empirical investigation of the "duplication and divergence" theory of protein evolution. PMID:14562959
A novel extracellular multicopper oxidase from Phanerochaete chrysosporium with ferroxidase activity. PMID:14532088
Visualisation and graph-theoretic analysis of a large-scale protein structural interactome. PMID:14531933
Human RNA polymerase II is partially blocked by DNA adducts derived from tumorigenic benzo[c]phenanthrene diol epoxides: relating biological consequences to conformational preferences. PMID:14530448
Matching protein structures with fuzzy alignments. PMID:14526099
Molecular dynamics simulations of galectin-1-oligosaccharide complexes reveal the molecular basis for ligand diversity. PMID:14517974
Structural and functional characterization of the human CCR5 receptor in complex with HIV gp120 envelope glycoprotein and CD4 receptor by molecular modeling studies. PMID:14517611
Molecular modelling of S1 and S2 subunits of SARS coronavirus spike glycoprotein. PMID:14511651
A structural model that explains the effects of hyperglycemia on collagenolysis. PMID:14507685
Statistical density modification using local pattern matching. PMID:14501107
Beta edge strands in protein structure prediction and aggregation. PMID:14500893
Exploring the sequence-structure protein landscape in the glycosyltransferase family. PMID:14500887
Finding evolutionary relations beyond superfamilies: fold-based superfamilies. PMID:14500881
A consensus view of fold space: combining SCOP, CATH, and the Dali Domain Dictionary. PMID:14500873
The 2.2 A resolution structure of RpiB/AlsB from Escherichia coli illustrates a new approach to the ribose-5-phosphate isomerase reaction. PMID:14499611
The calcium binding loops of the cytosolic phospholipase A2 C2 domain specify targeting to Golgi and ER in live cells. PMID:13679516
Diversity of core antigen epitopes of hepatitis B virus. PMID:12954985
Position specific variation in the rate of evolution in transcription factor binding sites. PMID:12946282
Brownian dynamics simulations of the interaction of Chlamydomonas cytochrome f with plastocyanin and cytochrome c6. PMID:12944318
Low-frequency modes of peptides and globular proteins in solution observed by ultrafast OHD-RIKES spectroscopy. PMID:12944303
Project management system for structural and functional proteomics: Sesame. PMID:12943363
Crystal structure of the YajQ protein from Haemophilus influenzae reveals a tandem of RNP-like domains. PMID:12943362
Asymmetric mutation rates at enzyme-inhibitor interfaces: implications for the protein-protein docking problem. PMID:12931008
Discrete restraint-based protein modeling and the Calpha-trace problem. PMID:12931001
A graph-theory algorithm for rapid protein side-chain prediction. PMID:12930999
The solution structure of bovine pancreatic trypsin inhibitor at high pressure. PMID:12930996
Calculating pKa values in enzyme active sites. PMID:12930989
Matthews coefficient probabilities: Improved estimates for unit cell contents of proteins, DNA, and protein-nucleic acid complex crystals. PMID:12930986
Using evolutionary rates to investigate protein functional divergence and conservation. A case study of the carbonic anhydrases. PMID:12930737
Exploring the molecular basis of selectivity in A1 adenosine receptors agonists: a case study. PMID:12926854
Cyclin D1 repression of peroxisome proliferator-activated receptor gamma expression and transactivation. PMID:12917338
Crystal structure and functional analysis of Escherichia coli glutamate decarboxylase. PMID:12912902
RNA structure comparison, motif search and discovery using a reduced representation of RNA conformational space. PMID:12907716
Directed evolution of Thermus maltogenic amylase toward enhanced thermal resistance. PMID:12902281
Microenvironment analysis and identification of magnesium binding sites in RNA. PMID:12888505
Zinc and mechanical prowess in the jaws of Nereis, a marine worm. PMID:12886017
Calculation of mutational free energy changes in transition states for protein folding. PMID:12885664
TOUCHSTONE II: a new approach to ab initio protein structure prediction. PMID:12885659
The role of small intraprotein cavities in the catalytic cycle of bacteriorhodopsin. PMID:12885636
Structure-based prediction of potential binding and nonbinding peptides to HIV-1 protease. PMID:12885633
Molecular dynamics decomposition of temperature-dependent elastic neutron scattering by a protein solution. PMID:12885619
Target selection and determination of function in structural genomics. PMID:12880206
Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy. PMID:12878726
Drug Adverse Reaction Target Database (DART) : proteins related to adverse drug reactions. PMID:12862503
Sizing the protein translocation pathway of colicin Ia channels. PMID:12860927
Molecular dynamic simulation of the ligand-receptor complexes of the aminoterminal domain of the metabotropic glutamate receptor mGluR1. PMID:12856414
Molecular modeling of the ligand-binding domains of the NR3A and NR3B subunits of the NMDA receptor. PMID:12856411
Molecular modeling of the chromatosome particle. PMID:12853645
Comparative protein structure modeling by iterative alignment, model building and model assessment. PMID:12853614
The structure of the cell cycle protein Cdc14 reveals a proline-directed protein phosphatase. PMID:12853468
Crystal structure of the carboxyltransferase subunit of the bacterial sodium ion pump glutaconyl-coenzyme A decarboxylase. PMID:12853465
Malignant brain tumor repeats: a three-leaved propeller architecture with ligand/peptide binding pockets. PMID:12842041
Structural study of binding of flagellin by Toll-like receptor 5. PMID:12837800
Structure of Mycobacterium tuberculosis methionine sulfoxide reductase A in complex with protein-bound methionine. PMID:12837786
Crystal structure of the YchF protein reveals binding sites for GTP and nucleic acid. PMID:12837776
Contribution of structural genomics to understanding the biology of Escherichia coli. PMID:12837772
Identification of protein functions from a molecular surface database, eF-site. PMID:12836670
Differential effects of supplementary affinity tags on the solubility of MBP fusion proteins. PMID:12836665
Protein Alpha Shape Similarity Analysis (PASSA): a new method for mapping protein binding sites. Application in the design of a selective inhibitor of tyrosine kinase 2. PMID:12825796
Development of biologically active compounds by combining 3D QSAR and structure-based design methods. PMID:12825795
Flexsim-R: a virtual affinity fingerprint descriptor to calculate similarities of functional groups. PMID:12825622
Distilling the essential features of a protein surface for improving protein-ligand docking, scoring, and virtual screening. PMID:12825621
Sensitivity of molecular docking to induced fit effects in influenza virus neuraminidase. PMID:12825619
Predicting the topology of transmembrane helical proteins using mean burial propensity and a hidden-Markov-model-based method. PMID:12824500
SiteLight: binding-site prediction using phage display libraries. PMID:12824481
UniqueProt: Creating representative protein sequence sets. PMID:12824419
Bioverse: Functional, structural and contextual annotation of proteins and proteomes. PMID:12824406
Static benchmarking of membrane helix predictions. PMID:12824384
Tools for the automatic identification and classification of RNA base pairs. PMID:12824344
STING Millennium: A web-based suite of programs for comprehensive and simultaneous analysis of protein structure and sequence. PMID:12824333
SEM (Symmetry Equivalent Molecules): A web-based GUI to generate and visualize the macromolecules. PMID:12824326
MolSurfer: A macromolecular interface navigator. PMID:12824324
Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures. PMID:12824322
LOC3D: annotate sub-cellular localization for protein structures. PMID:12824321
3MATRIX and 3MOTIF: a protein structure visualization system for conserved sequence motifs. PMID:12824319
WebFEATURE: An interactive web tool for identifying and visualizing functional sites on macromolecular structures. PMID:12824318
ESPript/ENDscript: Extracting and rendering sequence and 3D information from atomic structures of proteins. PMID:12824317
EVA: Evaluation of protein structure prediction servers. PMID:12824315
The PredictProtein server. PMID:12824312
PROTINFO: Secondary and tertiary protein structure prediction. PMID:12824311
DSSPcont: Continuous secondary structure assignments for proteins. PMID:12824310
Mouse proteome analysis. PMID:12819131
Understanding folding and design: replica-exchange simulations of "Trp-cage" miniproteins. PMID:12808142
CtBP/BARS: a dual-function protein involved in transcription co-repression and Golgi membrane fission. PMID:12805226
NMR structure of the active conformation of the Varkud satellite ribozyme cleavage site. PMID:12782785
Structure of Rhodococcus erythropolis limonene-1,2-epoxide hydrolase reveals a novel active site. PMID:12773375
Rapid and accurate calculation of protein 1H, 13C and 15N chemical shifts. PMID:12766419
BioMagResBank database with sets of experimental NMR constraints corresponding to the structures of over 1400 biomolecules deposited in the Protein Data Bank. PMID:12766409
Reduced hybrid cluster proteins (HCP) from Desulfovibrio desulfuricans ATCC 27774 and Desulfovibrio vulgaris (Hildenborough): X-ray structures at high resolution using synchrotron radiation. PMID:12764602
The long-range electrostatic interactions control tRNA-aminoacyl-tRNA synthetase complex formation. PMID:12761395
WaterScore: a novel method for distinguishing between bound and displaceable water molecules in the crystal structure of the binding site of protein-ligand complexes. PMID:12756610
Structural basis of regulation and substrate specificity of protein kinase CK2 deduced from the modeling of protein-protein interactions. PMID:12740046
A TyrCD1/TrpG8 hydrogen bond network and a TyrB10TyrCD1 covalent link shape the heme distal site of Mycobacterium tuberculosis hemoglobin O. PMID:12719529
Molecular modeling and functional mapping of B7-H1 and B7-DC uncouple costimulatory function from PD-1 interaction. PMID:12719480
A novel member of the split betaalphabeta fold: Solution structure of the hypothetical protein YML108W from Saccharomyces cerevisiae. PMID:12717036
Discovery of a significant, nontopological preference for antiparallel alignment of helices with parallel regions in sheets. PMID:12717033
Improved amino acid flexibility parameters. PMID:12717028
Cyclic coordinate descent: A robotics algorithm for protein loop closure. PMID:12717019
Modeling the hydration of proteins: prediction of structural and hydrodynamic parameters from X-ray diffraction and scattering data. PMID:12715248
Identifying residue-residue clashes in protein hybrids by using a second-order mean-field approach. PMID:12700353
Characterization of Saccharomyces cerevisiae protein Ser/Thr phosphatase T1 and comparison to its mammalian homolog PP5. PMID:12694636
Crystal structure of Swine vesicular disease virus and implications for host adaptation. PMID:12692248
Amino acid empirical contact energy definitions for fold recognition in the space of contact maps. PMID:12689348
Structural and functional characterization of recombinant mouse annexin A11: influence of calcium binding. PMID:12689336
A network of rice genes associated with stress response and seed development. PMID:12684538
Bioinformatics methods to predict protein structure and function. A practical approach. PMID:12632698
Discrimination of native protein structures using atom-atom contact scoring. PMID:12631702
Antibacterial properties of the sperm-binding proteins and peptides of human epididymis 2 (HE2) family; salt sensitivity, structural dependence and their interaction with outer and cytoplasmic membranes of Escherichia coli. PMID:12628001
Two families of mechanosensitive channel proteins. PMID:12626684
Novel mutations in the RFXANK gene: RFX complex containing in-vitro-generated RFXANK mutant binds the promoter without transactivating MHC II. PMID:12618906
Application of singular value decomposition to the analysis of time-resolved macromolecular x-ray data. PMID:12609912
Role of hydrophobic clusters and long-range contact networks in the folding of (alpha/beta)8 barrel proteins. PMID:12609894
Computer simulations of membrane protein folding: structure and dynamics. PMID:12609892
Development of unified statistical potentials describing protein-protein interactions. PMID:12609891
Novel mutant human fibronectin FIII9-10 domain pair with increased conformational stability and biological activity. PMID:12601142
Protein concerted motions in the DNA-human topoisomerase I complex. PMID:12595561
X-ray structure of the AAC(6')-Ii antibiotic resistance enzyme at 1.8 A resolution; examination of oligomeric arrangements in GNAT superfamily members. PMID:12592013
A novel iron centre in the split-Soret cytochrome c from Desulfovibrio desulfuricans ATCC 27774. PMID:12589573
The crystallographic model of rhodopsin and its use in studies of other G protein-coupled receptors. PMID:12574068
Future directions in protein function prediction. PMID:12549818
An empirical correlation between secondary structure content and averaged chemical shifts in proteins. PMID:12547802
Structural composition of betaI- and betaII-proteins. PMID:12538903
Fluorescence determination of tryptophan side-chain accessibility and dynamics in triple-helical collagen-like peptides. PMID:12524302
19 A solution structure of the filarial nematode immunomodulatory protein, ES-62. PMID:12524301
RNABase: an annotated database of RNA structures. PMID:12520063
The PSSH database of alignments between protein sequences and tertiary structures. PMID:12520061
PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB) in 2003. PMID:12520060
The Protein Data Bank and structural genomics. PMID:12520059
Integration of related sequences with protein three-dimensional structural families in an updated version of PALI database. PMID:12520058
MolMovDB: analysis and visualization of conformational change and structural flexibility. PMID:12520056
Enlarged FAMSBASE: protein 3D structure models of genome sequences for 41 species. PMID:12520053
E-MSD: the European Bioinformatics Institute Macromolecular Structure Database. PMID:12520052
The Proteome Analysis database: a tool for the in silico analysis of whole proteomes. PMID:12520037
PEP: Predictions for Entire Proteomes. PMID:12520036
ProtoNet: hierarchical classification of the protein space. PMID:12520020
KDBI: Kinetic Data of Bio-molecular Interactions database. PMID:12519995
The PEDANT genome database. PMID:12519983
Database resources of the National Center for Biotechnology. PMID:12519941
Biochemical filtering of a protein-protein docking simulation identifies the structure of a complex between a recombinant antibody fragment and alpha-bungarotoxin. PMID:12519078
Structure of Escherichia coli ribose-5-phosphate isomerase: a ubiquitous enzyme of the pentose phosphate pathway and the Calvin cycle. PMID:12517338
Automated side-chain model building and sequence assignment by template matching. PMID:12499538
Automated main-chain model building by template matching and iterative fragment extension. PMID:12499537
Structure of poly(ethylene glycol)-modified horseradish peroxidase in organic solvents: infrared amide I spectral changes upon protein dehydration are largely caused by protein structural changes and not by water removal per se. PMID:12496131
Movement of the C-helix during the gating of cyclic nucleotide-gated channels. PMID:12496096
Molecular dynamics study of Desulfovibrio africanus cytochrome c3 in oxidized and reduced forms. PMID:12496077
Structure modeling of the chemokine receptor CCR5: implications for ligand binding and selectivity. PMID:12496074
Tripeptide analysis of protein structures. PMID:12495440
A software tool for the prediction of Xaa-Pro peptide bond conformations in proteins based on 13C chemical shift statistics. PMID:12495031
SPINS: standardized protein NMR storage. A data dictionary and object-oriented relational database for archiving protein NMR spectra. PMID:12495027
beta-Glucosidase in cellulosome of the anaerobic fungus Piromyces sp. strain E2 is a family 3 glycoside hydrolase. PMID:12485115
A Hoogsteen base pair embedded in undistorted B-DNA. PMID:12466549
Probing the folding free energy landscape of the Src-SH3 protein domain. PMID:12446834
Extension of a local backbone description using a structural alphabet: a new approach to the sequence-structure relationship. PMID:12441385
Side-chain conformational entropy at protein-protein interfaces. PMID:12441384
Rapid protein domain assignment from amino acid sequence using predicted secondary structure. PMID:12441380
Thoroughly sampling sequence space: large-scale protein design of structural ensembles. PMID:12441379
Transmembrane helix predictions revisited. PMID:12441377
Long membrane helices and short loops predicted less accurately. PMID:12441376
Structural characterization of the human proteome. PMID:12421749
SeqHound: biological sequence and structure database as a platform for bioinformatics research. PMID:12401134
HEPT derivatives as non-nucleoside inhibitors of HIV-1 reverse transcriptase: QSAR studies agree with the crystal structures. PMID:12400858
Recovery of known T-cell epitopes by computational scanning of a viral genome. PMID:12400854
Protein kinase CK2: structure, regulation and role in cellular decisions of life and death. PMID:12396231
Common features in structures and sequences of sandwich-like proteins. PMID:12384574
A statistically derived parameterization for the collagen triple-helix. PMID:12381857
Construction of a fluorescent biosensor family. PMID:12381848
Construction and characterization of protein libraries composed of secondary structure modules. PMID:12381846
Synergistic activity of the ninth and tenth FIII domains of human fibronectin depends upon structural stability. PMID:12376529
Folding free energy function selects native-like protein sequences in the core but not on the surface. PMID:12368470
A comparison of profile hidden Markov model procedures for remote homology detection. PMID:12364612
RNA canonical and non-canonical base pairing types: a recognition method and complete repertoire. PMID:12364604
Investigation of the metal binding site in methionine aminopeptidase by density functional theory. PMID:12363216
Aggregation and self-assembly of hydrophobins from Trichoderma reesei: low-resolution structural models. PMID:12324441
Copper-mediated dimerization of CopZ, a predicted copper chaperone from Bacillus subtilis. PMID:12238948
A comparison of methods for calculating NMR cross-relaxation rates (NOESY and ROESY intensities) in small peptides. PMID:12238590
Drug resistance in HIV-1 protease: Flexibility-assisted mechanism of compensatory mutations. PMID:12237461
High resolution crystal structure of domain I of the Saccharomyces cerevisiae homing endonuclease PI-SceI. PMID:12235380
Human non-synonymous SNPs: server and survey. PMID:12202775
Efficient generation of feasible pathways for protein conformational transitions. PMID:12202386
Exploring the propensities of helices in PrP(C) to form beta sheet using NMR structures and sequence alignments. PMID:12202354
Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline. PMID:12193646
Plasticity in structure and interactions is critical for the action of indolicidin, an antibacterial peptide of innate immune origin. PMID:12192071
A structurally conserved water molecule in Rossmann dinucleotide-binding domains. PMID:12192068
Flexible docking under pharmacophore type constraints. PMID:12188022
Can we separate active from inactive conformations? PMID:12188020
A protein folding potential that places the native states of a large number of proteins near a local minimum. PMID:12165098
Thermodynamic environments in proteins: fundamental determinants of fold specificity. PMID:12142449
Bovine leukemia virus SU protein interacts with zinc, and mutations within two interacting regions differently affect viral fusion and infectivity in vivo. PMID:12134000
Relaxation kinetics and the glassiness of proteins: the case of bovine pancreatic trypsin inhibitor. PMID:12124257
Modeling shape and topology of low-resolution density maps of biological macromolecules. PMID:12124252
Crystal structure of monomeric human beta-2-microglobulin reveals clues to its amyloidogenic properties. PMID:12119416
Genomic evidence that the intracellular proteins of archaeal microbes contain disulfide bonds. PMID:12107280
RNAML: a standard syntax for exchanging RNA information. PMID:12088144
TRILOGY: Discovery of sequence-structure patterns across diverse proteins. PMID:12084910
A novel pollen-specific alpha-tubulin in sunflower: structure and characterization. PMID:12081369
Accurate representation of B-DNA double helical structure with implicit solvent and counterions. PMID:12080128
Interaction of cardiotoxins with membranes: a molecular modeling study. PMID:12080107
An intron-containing glycoside hydrolase family 9 cellulase gene encodes the dominant 90 kDa component of the cellulosome of the anaerobic fungus Piromyces sp. strain E2. PMID:12071852
The fibril_one on-line database: mutations, experimental conditions, and trends associated with amyloid fibril formation. PMID:12070339
Ligatoxin B, a new cytotoxic protein with a novel helix-turn-helix DNA-binding domain from the mistletoe Phoradendron liga. PMID:12049612
Structural basis for broad substrate specificity in higher plant beta-D-glucan glucohydrolases. PMID:12034895
Homology modeling and molecular dynamics study of NAD-dependent glycerol-3-phosphate dehydrogenase from Trypanosoma brucei rhodesiense, a potential target enzyme for anti-sleeping sickness drug development. PMID:12023213
An improved hydrogen bond potential: impact on medium resolution protein structures. PMID:12021440
Multiple mutagenesis of non-universal serine codons of the Candida rugosa LIP2 gene and biochemical characterization of purified recombinant LIP2 lipase overexpressed in Pichia pastoris. PMID:12020350
Intermolecular relaxation has little effect on intra-peptide exchange-transferred NOE intensities. PMID:12018479
Search and retrieve. Large-scale data generation is becoming increasingly important in biological research. But how good are the tools to make sense of the data? PMID:11991940
One site fits both: a model for the ternary complex of folate + NADPH in R67 dihydrofolate reductase, a D2 symmetric enzyme. PMID:11989624
Interrogating protein interaction networks through structural biology. PMID:11972061
Structural similarity to link sequence space: new potential superfamilies and implications for structural genomics. PMID:11967367
Computational studies on prion proteins: effect of Ala(117)-->Val mutation. PMID:11964260
Ab initio protein structure prediction on a genomic scale: application to the Mycoplasma genitalium genome. PMID:11959918
RNA:(guanine-N2) methyltransferases RsmC/RsmD and their homologs revisited--bioinformatic analysis and prediction of the active site based on the uncharacterized Mj0882 protein structure. PMID:11929612
Sequence similarities and evolutionary relationships of influenza virus A hemagglutinins. PMID:11928990
Structural analysis of conserved base pairs in protein-DNA complexes. PMID:11917033
Improved affinity of engineered streptavidin for the Strep-tag II peptide is due to a fixed open conformation of the lid-like loop at the binding site. PMID:11910031
Protein unfolding: rigidity lost. PMID:11891336
Inference of functional regions in proteins by quantification of evolutionary constraints. PMID:11880638
Natural beta-sheet proteins use negative design to avoid edge-to-edge aggregation. PMID:11880627
Gene3D: structural assignment for whole genes and genomes using the CATH domain structure database. PMID:11875040
Transient exposure of hydrophobic surface in the photoactive yellow protein monitored with Nile Red. PMID:11867475
Temperature dependence of protein dynamics: computer simulation analysis of neutron scattering properties. PMID:11867439
Molecular modeling and dynamics of the sodium channel inactivation gate. PMID:11867438
Surviving in a sea of data: a survey of plant genome data resources and issues in building data management systems. PMID:11860214
Electrostatics in protein-protein docking. PMID:11847280
Structural diversity of heparan sulfate binding domains in chemokines. PMID:11830659
Functional motions of influenza virus hemagglutinin: a structure-based analytical approach. PMID:11806902
A stochastic algorithm for global optimization and for best populations: a test case of side chains in proteins. PMID:11792838
Statistical potentials for fold assessment. PMID:11790853
Recursive domains in proteins. PMID:11790851
Crystal structure of the Yersinia pestis GTPase activator YopE. PMID:11790850
Persistently conserved positions in structurally similar, sequence dissimilar proteins: roles in preserving protein fold and function. PMID:11790845
Side-chain modeling with an optimized scoring function. PMID:11790842
Toward genomic identification of beta-barrel membrane proteins: composition and architecture of known structures. PMID:11790840
The CATH extended protein-family database: providing structural annotations for genome sequences. PMID:11790833
Functional evolution of two subtly different (similar) folds. PMID:11782293
Free energy force field (FEFF) 3D-QSAR analysis of a set of Plasmodium falciparum dihydrofolate reductase inhibitors. PMID:11776291
Rapid protein fold determination using secondary chemical shifts and cross-hydrogen bond 15N-13C' scalar couplings (3hbJNC'). PMID:11775739
Chimeric Vitreoscilla hemoglobin (VHb) carrying a flavoreductase domain relieves nitrosative stress in Escherichia coli: new insight into the functional role of VHb. PMID:11772621
BETAWRAP: successful prediction of parallel beta -helices from primary sequence reveals an association with many microbial pathogens. PMID:11752429
TTD: Therapeutic Target Database. PMID:11752352
SCOR: a Structural Classification of RNA database. PMID:11752346
MDB: the Metalloprotein Database and Browser at The Scripps Research Institute. PMID:11752342
ProTherm, Thermodynamic Database for Proteins and Mutants: developments in version 3.0. PMID:11752320
GTOP: a database of protein structures predicted from genome sequences. PMID:11752318
ASTRAL compendium enhancements. PMID:11752310
MODBASE, a database of annotated comparative protein structure models. PMID:11752309
The IMB Jena Image Library of Biological Macromolecules: 2002 update. PMID:11752308
The Protein Data Bank: unifying the archive. PMID:11752306
FIMM, a database of functional molecular immunology: update 2002. PMID:11752300
ASPD (Artificially Selected Proteins/Peptides Database): a database of proteins and peptides evolved in vitro. PMID:11752292
Annotating the human proteome: the Human Proteome Survey Database (HumanPSD) and an in-depth target database for G protein-coupled receptors (GPCR-PD) from Incyte Genomics. PMID:11752275
The Protein Information Resource: an integrated public resource of functional annotation of proteins. PMID:11752247
Database resources of the National Center for Biotechnology Information: 2002 update. PMID:11752242
The anti-toxin ParD of plasmid RK2 consists of two structurally distinct moieties and belongs to the ribbon-helix-helix family of DNA-binding proteins. PMID:11743881
Oligomerization of green fluorescent protein in the secretory pathway of endocrine cells. PMID:11736655
Map-likelihood phasing. PMID:11717488
Protein threading by learning. PMID:11717394
Analysis of crystal structures of aspartic proteinases: on the role of amino acid residues adjacent to the catalytic site of pepsin-like enzymes. PMID:11714911
The xenograft antigen bound to Griffonia simplicifolia lectin 1-B(4). X-ray crystal structure of the complex and molecular dynamics characterization of the binding site. PMID:11714721
Virus Particle Explorer (VIPER), a website for virus capsid structures and their computational analyses. PMID:11711584
Structural genomics of enzymes involved in sterol/isoprenoid biosynthesis. PMID:11698677
X-ray structure of the orphan nuclear receptor RORbeta ligand-binding domain in the active conformation. PMID:11689423
A thermodynamic framework for Mg2+ binding to RNA. PMID:11675490
THEMATICS: a simple computational predictor of enzyme function from structure. PMID:11606719
Reassignment of specificities of two cap methyltransferase domains in the reovirus lambda 2 protein. PMID:11574057
Comparing function and structure between entire proteomes. PMID:11567088
An integrated software suite for surface-based analyses of cerebral cortex. PMID:11522765
Circularly permuted proteins in the protein structure database. PMID:11514678
NMR of hydrogen bonding in cold-shock protein A and an analysis of the influence of crystallographic resolution on comparisons of hydrogen bond lengths. PMID:11514676
Arginine-140 and isoleucine-141 determine the 17beta-estradiol-binding specificity of the sex-steroid-binding protein (SBP, or SHBG) of human plasma. PMID:11514672
Structure of pyruvate dehydrogenase kinase. Novel folding pattern for a serine protein kinase. PMID:11483605
Mycobacterium tuberculosis hemoglobin N displays a protein tunnel suited for O2 diffusion to the heme. PMID:11483493
How common is the funnel-like energy landscape in protein-protein interactions? PMID:11468354
Modeling of the structural features of integral-membrane proteins reverse-environment prediction of integral membrane protein structure (REPIMPS). PMID:11468350
Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. PMID:11452024
Crystal structure of the M-fragment of alpha-catenin: implications for modulation of cell adhesion. PMID:11447106
RCSB Protein Data Bank: Improved Annotation, Search, and Visualization of Membrane Protein Structures Archived in the PDB PubMed citations: 1.

1 articles citing: RCSB Protein Data Bank: Improved Annotation, Search, and Visualization of Membrane Protein Structures Archived in the PDB

RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D. PMID:34676613
https://doi.org/10.1093/nar/gkaa1038

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deoxyribonucleic acid
metasource: Fairsharing.org
version: FAIRsharing.org: RCSB PDB; RCSB Protein Data Bank; DOI: https://doi.org/10.25504/FAIRsharing.2t35ja; Last edited: April 26, 2021, 2:57 p.m.; Last accessed: Jan 03 2022 7:05 p.m.

molecular structure
metasource: Fairsharing.org
version: FAIRsharing.org: RCSB PDB; RCSB Protein Data Bank; DOI: https://doi.org/10.25504/FAIRsharing.2t35ja; Last edited: April 26, 2021, 2:57 p.m.; Last accessed: Jan 03 2022 7:05 p.m.

protein
metasource: Fairsharing.org
version: FAIRsharing.org: RCSB PDB; RCSB Protein Data Bank; DOI: https://doi.org/10.25504/FAIRsharing.2t35ja; Last edited: April 26, 2021, 2:57 p.m.; Last accessed: Jan 03 2022 7:05 p.m.

metasource: re3data.org
version: re3data.org: RCSB Protein Data Bank; editing status 2021-09-09; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3KK66 last accessed: 2022-11-04

ribonucleic acid
metasource: Fairsharing.org
version: FAIRsharing.org: RCSB PDB; RCSB Protein Data Bank; DOI: https://doi.org/10.25504/FAIRsharing.2t35ja; Last edited: April 26, 2021, 2:57 p.m.; Last accessed: Jan 03 2022 7:05 p.m.

structure
metasource: Fairsharing.org
version: FAIRsharing.org: RCSB PDB; RCSB Protein Data Bank; DOI: https://doi.org/10.25504/FAIRsharing.2t35ja; Last edited: April 26, 2021, 2:57 p.m.; Last accessed: Jan 03 2022 7:05 p.m.

structure databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

protein structure
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

biological macromolecular resource
metasource: re3data.org
version: re3data.org: RCSB Protein Data Bank; editing status 2021-09-09; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3KK66 last accessed: 2022-11-04

covid-19
metasource: re3data.org
version: re3data.org: RCSB Protein Data Bank; editing status 2021-09-09; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3KK66 last accessed: 2022-11-04

membrane and lipoproteins
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:27.464785

small molecules
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:27.464785

protein structure analysis
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:27.464785

enzymes
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version: extracted_at: 2022-11-04T11:24:27.464785

protein sites, features and motifs
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:27.464785

dna molecular structure protein rna structure structure protein structure biological macromolecular resource covid-19 membrane and lipoproteins small molecule protein structure analysis enzyme protein sites, features and motifs

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