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Improving Docking Results via Reranking of Ensembles of Ligand Poses in Multiple X-ray Protein Conformations with MM-GBSA

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What this work says

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

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Flexible protein–ligand docking by global energy optimization in internal coordinates

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Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database

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Improved protein–ligand docking using GOLD

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A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance

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Comparative evaluation of eight docking tools for docking and virtual screening accuracy

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Comparing protein–ligand docking programs is difficult

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Protein–ligand docking: Current status and future challenges

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Ensemble docking of multiple protein structures: Considering protein structural variations in molecular docking

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The VSGB 2.0 model: A next generation energy model for high resolution protein structure modeling

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Applying conformational selection theory to improve crossdocking efficiency in 3‐phosphoinositide dependent protein kinase‐1

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Development and validation of a genetic algorithm for flexible docking 1 1Edited by F. E. Cohen

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KNIME: The Konstanz Information Miner

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Binding site characteristics in structure-based virtual screening: evaluation of current docking tools

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Effects of protein conformation in docking: improved pose prediction through protein pocket adaptation

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Surflex-Dock: Docking benchmarks and real-world application

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Are predefined decoy sets of ligand poses able to quantify scoring function accuracy?

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Pose prediction and virtual screening performance of GOLD scoring functions in a standardized test

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Variability in docking success rates due to dataset preparation

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Close intramolecular sulfur–oxygen contacts: modified force field parameters for improved conformation generation

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Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments

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A geometric approach to macromolecule-ligand interactions

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Impact of protein binding cavity volume (PCV) and ligand volume (LV) in rigid and flexible docking of protein–ligand complexes

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Essential considerations for using protein–ligand structures in drug discovery

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Protein Flexibility in Ligand Docking and Virtual Screening to Protein Kinases

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Testing a Flexible-receptor Docking Algorithm in a Model Binding Site

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Rescoring Docking Hit Lists for Model Cavity Sites: Predictions and Experimental Testing

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Binding of Small-Molecule Ligands to Proteins: “What You See” Is Not Always “What You Get”

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Consensus scoring for ligand/protein interactions

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Detailed Structural Analysis of Glycosidase/Inhibitor Interactions: Complexes of Cex from Cellulomonas fimi with Xylobiose-Derived Aza-Sugars,

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Consensus Scoring Criteria for Improving Enrichment in Virtual Screening

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Physics-Based Scoring of Protein−Ligand Complexes: Enrichment of Known Inhibitors in Large-Scale Virtual Screening

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ConfGen: A Conformational Search Method for Efficient Generation of Bioactive Conformers

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Protein Kinases: Docking and Homology Modeling Reliability

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Rapid Context-Dependent Ligand Desolvation in Molecular Docking

inferredcites →https://doi.org/10.1021/ci100354xopenalex-snapshot

Postprocessing of Docked Protein−Ligand Complexes Using Implicit Solvation Models

inferredcites →https://doi.org/10.1021/ci2002507openalex-snapshot

Cheminformatics Meets Molecular Mechanics: A Combined Application of Knowledge-Based Pose Scoring and Physical Force Field-Based Hit Scoring Functions Improves the Accuracy of Structure-Based Virtual Screening

inferredcites →https://doi.org/10.1021/ci2005934openalex-snapshot

Potential and Limitations of Ensemble Docking

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Numerical Errors and Chaotic Behavior in Docking Simulations

inferredcites →https://doi.org/10.1021/ci300399wopenalex-snapshot

Consensus Docking: Improving the Reliability of Docking in a Virtual Screening Context

inferredcites →https://doi.org/10.1021/ci300425vopenalex-snapshot

MM/GBSA Binding Energy Prediction on the PDBbind Data Set: Successes, Failures, and Directions for Further Improvement

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Boosting Virtual Screening Enrichments with Data Fusion: Coalescing Hits from Two-Dimensional Fingerprints, Shape, and Docking

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CSAR Benchmark Exercise 2011–2012: Evaluation of Results from Docking and Relative Ranking of Blinded Congeneric Series

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Toward Fully Automated High Performance Computing Drug Discovery: A Massively Parallel Virtual Screening Pipeline for Docking and Molecular Mechanics/Generalized Born Surface Area Rescoring to Improve Enrichment

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Virtual Screening of PRK1 Inhibitors: Ensemble Docking, Rescoring Using Binding Free Energy Calculation and QSAR Model Development

inferredcites →https://doi.org/10.1021/ci4007326openalex-snapshot

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inferredcites →https://doi.org/10.1021/ci500080qopenalex-snapshot

Comparative Assessment of Scoring Functions on an Updated Benchmark: 1. Compilation of the Test Set

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The Application of Statistical Methods to Cognate Docking: A Path Forward?

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Best of Both Worlds: On the Complementarity of Ligand-Based and Structure-Based Virtual Screening

inferredcites →https://doi.org/10.1021/ci7000346openalex-snapshot

Comparative Performance of Several Flexible Docking Programs and Scoring Functions: Enrichment Studies for a Diverse Set of Pharmaceutically Relevant Targets

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Lessons in Molecular Recognition. 2. Assessing and Improving Cross-Docking Accuracy

inferredcites →https://doi.org/10.1021/ci7004274openalex-snapshot

Cross-Docking of Inhibitors into CDK2 Structures. 1

inferredcites →https://doi.org/10.1021/ci700428dopenalex-snapshot

Cross-Docking of Inhibitors into CDK2 Structures. 2

inferredcites →https://doi.org/10.1021/ci700470copenalex-snapshot

Investigation of MM-PBSA Rescoring of Docking Poses

inferredcites →https://doi.org/10.1021/ci800004wopenalex-snapshot

MM-GB/SA Rescoring of Docking Poses in Structure-Based Lead Optimization

inferredcites →https://doi.org/10.1021/ci800084xopenalex-snapshot

An Alternative Method for the Evaluation of Docking Performance: RSR vs RMSD

inferredcites →https://doi.org/10.1021/ci8002254openalex-snapshot

Protein−Ligand Docking against Non-Native Protein Conformers

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inferredcites →https://doi.org/10.1021/ci9000053openalex-snapshot

Comparative Assessment of Scoring Functions on a Diverse Test Set

inferredcites →https://doi.org/10.1021/ci900022hopenalex-snapshot

QM/MM As a Tool in Fragment Based Drug Discovery. A Cross-Docking, Rescoring Study of Kinase Inhibitors

inferredcites →https://doi.org/10.1021/ci9000629openalex-snapshot

Effect of Input Differences on the Results of Docking Calculations

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GARD: A Generally Applicable Replacement for RMSD

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Prediction of Absolute Solvation Free Energies using Molecular Dynamics Free Energy Perturbation and the OPLS Force Field

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Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids

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Inclusion of Solvation in Ligand Binding Free Energy Calculations Using the Generalized-Born Model

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Lessons in Molecular Recognition: The Effects of Ligand and Protein Flexibility on Molecular Docking Accuracy

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Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy

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The PDBbind Database: Methodologies and Updates

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A Critical Assessment of Docking Programs and Scoring Functions

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Novel Procedure for Modeling Ligand/Receptor Induced Fit Effects

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Protein Structures in Virtual Screening: A Case Study with CDK2

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Benchmarking Sets for Molecular Docking

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Targeting epigenetic regulators: In-silico discovery of natural inhibitors against histone demethylase KDM4C

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