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Docking Ligands into Flexible and Solvated Macromolecules. 7. Impact of Protein Flexibility and Water Molecules on Docking-Based Virtual Screening Accuracy

https://doi.org/10.1021/ci500299h
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection—What can we learn from earlier mistakes?
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Recommendations for evaluation of computational methods
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Effects of protein conformation in docking: improved pose prediction through protein pocket adaptation
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Substantial improvements in large-scale redocking and screening using the novel HYDE scoring function
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Surflex-Dock: Docking benchmarks and real-world application
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Docking and scoring with ICM: the benchmarking results and strategies for improvement
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Pose prediction and virtual screening performance of GOLD scoring functions in a standardized test
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Docking performance of the glide program as evaluated on the Astex and DUD datasets: a complete set of glide SP results and selected results for a new scoring function integrating WaterMap and glide
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An ant colony optimization approach to flexible protein–ligand docking
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Virtual screening strategies in drug discovery
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Protein Flexibility in Ligand Docking and Virtual Screening to Protein Kinases
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Geometry-Based Sampling of Conformational Transitions in Proteins
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Integrating Medicinal Chemistry, Organic/Combinatorial Chemistry, and Computational Chemistry for the Discovery of Selective Estrogen Receptor Modulators with F orecaster , a Novel Platform for Drug Discovery
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Hydration Properties of Ligands and Drugs in Protein Binding Sites: Tightly-Bound, Bridging Water Molecules and Their Effects and Consequences on Molecular Design Strategies
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Docking Challenge: Protein Sampling and Molecular Docking Performance
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Evaluation and Optimization of Virtual Screening Workflows with DEKOIS 2.0 – A Public Library of Challenging Docking Benchmark Sets
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Docking Ligands into Flexible and Solvated Macromolecules. 6. Development and Application to the Docking of HDACs and other Zinc Metalloenzymes Inhibitors
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Docking Ligands into Flexible and Solvated Macromolecules. 1. Development and Validation of FITTED 1.0
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Evaluating Virtual Screening Methods: Good and Bad Metrics for the “Early Recognition” Problem
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Docking Ligands into Flexible and Solvated Macromolecules. 2. Development and Application of F itted 1.5 to the Virtual Screening of Potential HCV Polymerase Inhibitors
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Using Buriedness To Improve Discrimination between Actives and Inactives in Docking
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Empirical Scoring Functions for Advanced Protein−Ligand Docking with PLANTS
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Docking Ligands into Flexible and Solvated Macromolecules. 3. Impact of Input Ligand Conformation, Protein Flexibility, and Water Molecules on the Accuracy of Docking Programs
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Docking Ligands into Flexible and Solvated Macromolecules. 4. Are Popular Scoring Functions Accurate for this Class of Proteins?
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Comparison of Several Molecular Docking Programs: Pose Prediction and Virtual Screening Accuracy
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Docking Ligands into Flexible and Solvated Macromolecules. 5. Force-Field-Based Prediction of Binding Affinities of Ligands to Proteins
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Addressing Limitations with the MM-GB/SA Scoring Procedure using the WaterMap Method and Free Energy Perturbation Calculations
inferredcites →https://doi.org/10.1021/ct100504hopenalex-snapshot
Effects of Water Placement on Predictions of Binding Affinities for p38α MAP Kinase Inhibitors
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Thermodynamics of Water in an Enzyme Active Site: Grid-Based Hydration Analysis of Coagulation Factor Xa
inferredcites →https://doi.org/10.1021/jm050543popenalex-snapshot
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inferredcites →https://doi.org/10.1021/jm0608356openalex-snapshot
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inferredcites →https://doi.org/10.1021/jm100488wopenalex-snapshot
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inferredcites →https://doi.org/10.1021/jm2005145openalex-snapshot
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inferredcites →https://doi.org/10.1021/jm300687eopenalex-snapshot
Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking
inferredcites →https://doi.org/10.1021/jm800071vopenalex-snapshot
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inferredcites →https://doi.org/10.1021/jm8006239openalex-snapshot
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inferredcites →https://doi.org/10.1021/jp9047456openalex-snapshot
Prediction of the Water Content in Protein Binding Sites
inferredcites →https://doi.org/10.1021/jp961992ropenalex-snapshot
The GB/SA Continuum Model for Solvation. A Fast Analytical Method for the Calculation of Approximate Born Radii
inferredcites →https://doi.org/10.1038/sj.bjp.0707515openalex-snapshot
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Protein conformational space in higher order ϕ-Ψ maps
inferredcites →https://doi.org/10.1073/pnas.0511333103openalex-snapshot
A method for evaluating the structural quality of protein models by using higher-order φ–ψ pairs scoring
inferredcites →https://doi.org/10.1073/pnas.0610202104openalex-snapshot
Motifs for molecular recognition exploiting hydrophobic enclosure in protein–ligand binding
inferredcites →https://doi.org/10.1073/pnas.1016793108openalex-snapshot
Ligand binding to protein-binding pockets with wet and dry regions
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Transitions to catalytically inactive conformations in EGFR kinase
inferredcites →https://doi.org/10.1093/clinchem/39.4.561openalex-snapshot
Receiver-operating characteristic (ROC) plots: a fundamental evaluation tool in clinical medicine
inferredcites →https://doi.org/10.1093/nar/28.1.235openalex-snapshot
The Protein Data Bank
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Docking, virtual high throughput screening and in silico fragment‐based drug design
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What has virtual screening ever done for drug discovery?
inferredcites →https://doi.org/10.2165/00063030-200721010-00005openalex-snapshot
Structure-Based Virtual Screening of FGFR Inhibitors
inferredcites →https://doi.org/10.2174/156802609789207127openalex-snapshot
Structure-Based Drug Design Strategies in Medicinal Chemistry
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The Role of Water Molecules in Computational Drug Design
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Modeling Reality for Optimal Docking of Small Molecules to Biological Targets
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