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In pursuit of virtual lead optimization: The role of the receptor structure and ensembles in accurate docking

https://doi.org/10.1002/prot.22081

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What this work says

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

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Conformational sampling by NMR solution structures calculated with the program DIANA evaluated by comparison with long-time molecular dynamics calculations in explicit water

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Exploring the dynamic information content of a protein NMR structure: Comparison of a molecular dynamics simulation with the NMR and X-ray structures ofEscherichia coli ribonuclease HI

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The penultimate rotamer library

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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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A general approach for developing system‐specific functions to score protein–ligand docked complexes using support vector inductive logic programming

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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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Scoring noncovalent protein-ligand interactions: A continuous differentiable function tuned to compute binding affinities

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Solution Structure of Human Dihydrofolate Reductase in its Complex with Trimethoprim and NADPH

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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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Complexity and simplicity of ligand–macromolecule interactions: the energy landscape perspective

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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

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Structure and Hydride Transfer Mechanism of a Moderate Thermophilic Dihydrofolate Reductase from Bacillus stearothermophilus and Comparison to Its Mesophilic and Hyperthermophilic Homologues,

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Loop and Subdomain Movements in the Mechanism of Escherichia coli Dihydrofolate Reductase: Crystallographic Evidence,

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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,

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Ligand-Induced Conformational Changes in the Crystal Structures of Pneumocystis carinii Dihydrofolate Reductase Complexes with Folate and NADP + ,

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Screening Drug-Like Compounds by Docking to Homology Models: A Systematic Study

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Incorporating Dynamics in E. coli Dihydrofolate Reductase Enhances Structure-Based Drug Discovery

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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

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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/jm0300330openalex-snapshot

Information Decay in Molecular Docking Screens against Holo, Apo, and Modeled Conformations of Enzymes

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Prediction of Protein−Ligand Interactions. Docking and Scoring: Successes and Gaps

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Highly Efficient Ligands for Dihydrofolate Reductase from Cryptosporidium hominis and Toxoplasma gondii Inspired by Structural Analysis

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Developing a Dynamic Pharmacophore Model for HIV-1 Integrase

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Method for Including the Dynamic Fluctuations of a Protein in Computer-Aided Drug Design

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The sensitivity of the results of molecular docking to induced fit effects: Application to thrombin, thermolysin and neuraminidase

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Letter to the Editor: NMR-based solution structure of the complex of Lactobacillus casei dihydrofolate reductase with trimethoprim and NADPH

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Virtual screening of chemical libraries

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Structure of and kinetic channelling in bifunctional dihydrofolate reductase–thymidylate synthase

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Insights into antifolate resistance from malarial DHFR-TS structures

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Neutron diffraction studies of Escherichia coli dihydrofolate reductase complexed with methotrexate

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Geno3D: automatic comparative molecular modelling of protein

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ESyPred3D: Prediction of proteins 3D structures

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CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

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The Protein Data Bank

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SWISS-MODEL: an automated protein homology-modeling server

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Analysis of three crystal structure determinations of a 5-methyl-6-N-methylanilino pyridopyrimidine antifolate complex with human dihydrofolate reductase

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Two crystal structures of dihydrofolate reductase-thymidylate synthase fromCryptosporidium hominisreveal protein–ligand interactions including a structural basis for observed antifolate resistance

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Efficient molecular docking of NMR structures: Application to HIV‐1 protease

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Dicyclic and Tricyclic Diaminopyrimidine Derivatives as Potent Inhibitors of Cryptosporidium parvum Dihydrofolate Reductase: Structure-Activity and Structure-Selectivity Correlations

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NMR-based solution structure of the complex of Lactobacillus casei dihydrofolate reductase with trimethoprim and NADPH

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Predicting Molecular Interactions in silico: II. Protein-Protein and Protein- Drug Docking

What points at this work

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

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Docking Methods for Virtual Screening: Principles and Recent Advances

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Protein Flexibility in Structure‐Based Virtual Screening: From Models to Algorithms

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Virtual Screening and Biological Characterization of Novel Histone Arginine Methyltransferase PRMT1 Inhibitors

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In Pursuit of Fully Flexible Protein‐Ligand Docking: Modeling the Bilateral Mechanism of Binding

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

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Receptor flexibility in small‐molecule docking calculations

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Normal Mode-Based Approaches in Receptor Ensemble Docking

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How to choose relevant multiple receptor conformations for virtual screening: a test case of Cdk2 and normal mode analysis

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Computational fragment-based screening using RosettaLigand: the SAMPL3 challenge

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Open challenges in structure-based virtual screening: Receptor modeling, target flexibility consideration and active site water molecules description

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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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Protein flexibility in docking and surface mapping

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Cosolvent and Dynamic Effects in Binding Pocket Search by Docking Simulations

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A Pipeline To Enhance Ligand Virtual Screening: Integrating Molecular Dynamics and Fingerprints for Ligand and Proteins

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Inexpensive Method for Selecting Receptor Structures for Virtual Screening

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Cosolvent-Based Molecular Dynamics for Ensemble Docking: Practical Method for Generating Druggable Protein Conformations

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Ligand-Binding-Site Structure Refinement Using Molecular Dynamics with Restraints Derived from Predicted Binding Site Templates

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Predictive Power of Molecular Dynamics Receptor Structures in Virtual Screening

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Discovery of Novel Checkpoint Kinase 1 Inhibitors by Virtual Screening Based on Multiple Crystal Structures

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Potential and Limitations of Ensemble Docking

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Novel Inhibitor Discovery through Virtual Screening against Multiple Protein Conformations Generated via Ligand-Directed Modeling: A Maternal Embryonic Leucine Zipper Kinase Example

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Scoring Ensembles of Docked Protein:Ligand Interactions for Virtual Lead Optimization

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Recipes for the Selection of Experimental Protein Conformations for Virtual Screening

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Structure-Based Approach to the Development of Potent and Selective Inhibitors of Dihydrofolate Reductase from Cryptosporidium

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