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