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