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In pursuit of virtual lead optimization: Pruning ensembles of receptor structures for increased efficiency and accuracy during docking

https://doi.org/10.1002/prot.22214
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Towards in silico lead optimization: Scores from ensembles of protein/ligand conformations reliably correlate with biological activity
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Evaluating the potency of HIV‐1 protease drugs to combat resistance
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In pursuit of virtual lead optimization: The role of the receptor structure and ensembles in accurate docking
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Computational studies of ligand diffusion in globins: I. Leghemoglobin
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The crystal structure of dihydrofolate reductase from Thermotoga maritima: molecular features of thermostability
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An improved relaxed complex scheme for receptor flexibility in computer-aided drug design
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Improving database enrichment through ensemble docking
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Solution Structure of Human Dihydrofolate Reductase in its Complex with Trimethoprim and NADPH
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Suppression of HIV-1 Protease Inhibitor Resistance by Phosphonate-mediated Solvent Anchoring
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Ultra-high Resolution Crystal Structure of HIV-1 Protease Mutant Reveals Two Binding Sites for Clinical Inhibitor TMC114
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Molecular Dynamics Studies on the HIV-1 Integrase Catalytic Domain
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Replica-exchange molecular dynamics method for protein folding
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Crystal structures of Escherichia coli and Lactobacillus casei dihydrofolate reductase refined at 1.7 A resolution. I. General features and binding of methotrexate.
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Atomic Structures of Human Dihydrofolate Reductase Complexed with NADPH and Two Lipophilic Antifolates at 1.09Å and 1.05Å Resolution
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Crystal Structure of the Conserved Core of HIV-1 Nef Complexed with a Src Family SH3 Domain
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Complexity and simplicity of ligand–macromolecule interactions: the energy landscape perspective
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The structure of Pneumocystis carinii dihydrofolate reductase to 1.9 å resolution
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Protein flexibility and drug design: how to hit a moving target
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Isomorphous Crystal Structures of Escherichia coli Dihydrofolate Reductase Complexed with Folate, 5-Deazafolate, and 5,10-Dideazatetrahydrofolate: Mechanistic Implications
inferredcites →https://doi.org/10.1021/bi026369dopenalex-snapshot
Coupling Interactions of Distal Residues Enhance Dihydrofolate Reductase Catalysis: Mutational Effects on Hydride Transfer Rates
inferredcites →https://doi.org/10.1021/bi050630jopenalex-snapshot
Structure and Hydride Transfer Mechanism of a Moderate Thermophilic Dihydrofolate Reductase from Bacillus stearothermophilus and Comparison to Its Mesophilic and Hyperthermophilic Homologues,
inferredcites →https://doi.org/10.1021/bi700822gopenalex-snapshot
Caught in the Act: The 1.5 Å Resolution Crystal Structures of the HIV-1 Protease and the I54V Mutant Reveal a Tetrahedral Reaction Intermediate
inferredcites →https://doi.org/10.1021/bi962337copenalex-snapshot
Loop and Subdomain Movements in the Mechanism of Escherichia coli Dihydrofolate Reductase: Crystallographic Evidence,
inferredcites →https://doi.org/10.1021/bi971711lopenalex-snapshot
Comparison of Two Independent Crystal Structures of Human Dihydrofolate Reductase Ternary Complexes Reduced with Nicotinamide Adenine Dinucleotide Phosphate and the Very Tight-Binding Inhibitor PT523,
inferredcites →https://doi.org/10.1021/bi982728mopenalex-snapshot
Ligand-Induced Conformational Changes in the Crystal Structures of Pneumocystis carinii Dihydrofolate Reductase Complexes with Folate and NADP + ,
inferredcites →https://doi.org/10.1021/ci700167nopenalex-snapshot
Incorporating Dynamics in E. coli Dihydrofolate Reductase Enhances Structure-Based Drug Discovery
inferredcites →https://doi.org/10.1021/ci7003626openalex-snapshot
Maximum Common Binding Modes (MCBM): Consensus Docking Scoring Using Multiple Ligand Information and Interaction Fingerprints
inferredcites →https://doi.org/10.1021/ja020429lopenalex-snapshot
Studying Enzyme Binding Specificity in Acetylcholinesterase Using a Combined Molecular Dynamics and Multiple Docking Approach
inferredcites →https://doi.org/10.1021/ja0469378openalex-snapshot
Incorporating Protein Flexibility in Structure-Based Drug Discovery: Using HIV-1 Protease as a Test Case
inferredcites →https://doi.org/10.1021/ja068256dopenalex-snapshot
Protein Flexibility and Species Specificity in Structure-Based Drug Discovery: Dihydrofolate Reductase as a Test System
inferredcites →https://doi.org/10.1021/ja073687xopenalex-snapshot
Small Molecule Inhibitors of the MDM2-p53 Interaction Discovered by Ensemble-Based Receptor Models
inferredcites →https://doi.org/10.1021/jm00349a003openalex-snapshot
Comparison of the inhibition of Escherichia coli and Lactobacillus casei dihydrofolate reductase by 2,4-diamino-5-(substituted-benzyl)pyrimidines: quantitative structure-activity relationships, x-ray crystallography, and computer graphics in structure-activity analysis
inferredcites →https://doi.org/10.1021/jm00368a006openalex-snapshot
Crystallography, quantitative structure-activity relationships, (QSAR) and molecular graphics in a comparative analysis of the inhibition of dihydrofolate reductase from chicken liver and Lactobacillus casei by 4,6-diamino-1,2-dihydro-2,2-dimethyl-1-(substituted-phenyl)-s-triazines
inferredcites →https://doi.org/10.1021/jm030331xopenalex-snapshot
Structural Interaction Fingerprint (SIFt): A Novel Method for Analyzing Three-Dimensional Protein−Ligand Binding Interactions
inferredcites →https://doi.org/10.1021/jm049560popenalex-snapshot
Discovery and Selection of TMC114, a Next Generation HIV-1 Protease Inhibitor
inferredcites →https://doi.org/10.1021/jm050540copenalex-snapshot
Novel Procedure for Modeling Ligand/Receptor Induced Fit Effects
inferredcites →https://doi.org/10.1021/jm060561mopenalex-snapshot
Structure-Based Design of Novel HIV-1 Protease Inhibitors To Combat Drug Resistance
inferredcites →https://doi.org/10.1021/jm990322hopenalex-snapshot
Developing a Dynamic Pharmacophore Model for HIV-1 Integrase
inferredcites →https://doi.org/10.1021/jp991997zopenalex-snapshot
Method for Including the Dynamic Fluctuations of a Protein in Computer-Aided Drug Design
inferredcites →https://doi.org/10.1023/a:1008015827877openalex-snapshot
The sensitivity of the results of molecular docking to induced fit effects: Application to thrombin, thermolysin and neuraminidase
inferredcites →https://doi.org/10.1023/a:1020659713373openalex-snapshot
Letter to the Editor: NMR-based solution structure of the complex of Lactobacillus casei dihydrofolate reductase with trimethoprim and NADPH
inferredcites →https://doi.org/10.1038/nsb0394-186openalex-snapshot
Structure of and kinetic channelling in bifunctional dihydrofolate reductase–thymidylate synthase
inferredcites →https://doi.org/10.1038/nsb921openalex-snapshot
Insights into antifolate resistance from malarial DHFR-TS structures
inferredcites →https://doi.org/10.1073/pnas.0604977103openalex-snapshot
Neutron diffraction studies of Escherichia coli dihydrofolate reductase complexed with methotrexate
inferredcites →https://doi.org/10.1093/bioinformatics/18.1.213openalex-snapshot
Geno3D: automatic comparative molecular modelling of protein
inferredcites →https://doi.org/10.1093/bioinformatics/18.9.1250openalex-snapshot
ESyPred3D: Prediction of proteins 3D structures
inferredcites →https://doi.org/10.1093/nar/22.22.4673openalex-snapshot
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
inferredcites →https://doi.org/10.1093/nar/gkg520openalex-snapshot
SWISS-MODEL: an automated protein homology-modeling server
inferredcites →https://doi.org/10.1107/s1744309105002435openalex-snapshot
Two crystal structures of dihydrofolate reductase-thymidylate synthase fromCryptosporidium hominisreveal protein–ligand interactions including a structural basis for observed antifolate resistance
inferredcites →https://doi.org/10.1111/j.1742-4658.2005.04923.xopenalex-snapshot
Molecular basis for substrate recognition and drug resistance from 1.1 to 1.6 Å resolution crystal structures of HIV‐1 protease mutants with substrate analogs
inferredcites →https://doi.org/10.1128/aac.45.12.3293-3303.2001openalex-snapshot
Dicyclic and Tricyclic Diaminopyrimidine Derivatives as Potent Inhibitors of Cryptosporidium parvum Dihydrofolate Reductase: Structure-Activity and Structure-Selectivity Correlations
inferredcites →https://doi.org/10.1128/jvi.01900-05openalex-snapshot
Role of Invariant Thr80 in Human Immunodeficiency Virus Type 1 Protease Structure, Function, and Viral Infectivity
inferredcites →https://doi.org/10.1128/jvi.02706-06openalex-snapshot
Unique Thermodynamic Response of Tipranavir to Human Immunodeficiency Virus Type 1 Protease Drug Resistance Mutations
inferredcites →https://doi.org/10.1128/mcb.01557-07openalex-snapshot
Acetylation of Conserved Lysines in the Catalytic Core of Cyclin-Dependent Kinase 9 Inhibits Kinase Activity and Regulates Transcription
inferredcites →https://doi.org/10.13018/bmr5396openalex-snapshot
NMR-based solution structure of the complex of Lactobacillus casei dihydrofolate reductase with trimethoprim and NADPH

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Induced fit docking, and the use of QM/MM methods in docking
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2,4-Diamino-5-(2′-arylpropargyl)pyrimidine derivatives as new nonclassical antifolates for human dihydrofolate reductase inhibition
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Knowledge-Based Methods To Train and Optimize Virtual Screening Ensembles
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Efficient Incorporation of Protein Flexibility and Dynamics into Molecular Docking Simulations
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