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A statistical rescoring scheme for protein–ligand docking: Consideration of entropic effect

https://doi.org/10.1002/prot.21844
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Calculation of absolute binding free energies for charged ligands and effects of long-range electrostatic interactions
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Predicting structural effects in HIV-1 protease mutant complexes with flexible ligand docking and protein side-chain optimization
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Side-chain flexibility in proteins upon ligand binding
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Reduced surface: An efficient way to compute molecular surfaces
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UCSF Chimera—A visualization system for exploratory research and analysis
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New and fast statistical‐thermodynamic method for computation of protein‐ligand binding entropy substantially improves docking accuracy
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Role of binding entropy in the refinement of protein–ligand docking predictions: Analysis based on the use of 11 scoring functions
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ICM—A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation
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Application of InChI to curate, index, and query 3‐D structures
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Mass spectrometry identification of NASP binding partners in HeLa cells
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Novel statistical‐thermodynamic methods to predict protein‐ligand binding positions using probability distribution functions
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Critical evaluation of methods to incorporate entropy loss upon binding in high‐throughput docking
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Absolute and relative binding free energy calculations of the interaction of biotin and its analogs with streptavidin using molecular dynamics/free energy perturbation approaches
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A Fast Flexible Docking Method using an Incremental Construction Algorithm
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FlexE: efficient molecular docking considering protein structure variations
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Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: conformationally flexible docking by evolutionary programming
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Testing a Flexible-receptor Docking Algorithm in a Model Binding Site
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Consensus scoring for ligand/protein interactions
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Calculating Structures and Free Energies of Complex Molecules: Combining Molecular Mechanics and Continuum Models
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Free Energy Simulations Come of Age: Protein−Ligand Recognition
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Protein-Based Virtual Screening of Chemical Databases. 1. Evaluation of Different Docking/Scoring Combinations
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Hierarchy of Simulation Models in Predicting Structure and Energetics of the Src SH2 Domain Binding to Tyrosyl Phosphopeptides
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Comparative Evaluation of 11 Scoring Functions for Molecular Docking
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A Knowledge-Based Energy Function for Protein−Ligand, Protein−Protein, and Protein−DNA Complexes
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A General and Fast Scoring Function for Protein−Ligand Interactions: A Simplified Potential Approach
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Consensus Scoring: A Method for Obtaining Improved Hit Rates from Docking Databases of Three-Dimensional Structures into Proteins
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DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases
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λ-dynamics: A new approach to free energy calculations
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What points at this work

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

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LigDockCSA: Protein–ligand docking using conformational space annealing
inferred← citeshttps://doi.org/10.1002/jcc.23438openalex-snapshot
GalaxyDock2: Protein–ligand docking using beta‐complex and global optimization
inferred← citeshttps://doi.org/10.1002/prot.22415openalex-snapshot
Automated site preparation in physics‐based rescoring of receptor ligand complexes
inferred← citeshttps://doi.org/10.1007/978-3-319-09976-7_11openalex-snapshot
Protein Ligand Docking in Drug Discovery
inferred← citeshttps://doi.org/10.1007/978-981-97-0814-7_10openalex-snapshot
Bioinformatics and Computational Biology
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Biostatistical Investigation Using Docking Mechanism and Its Database to Investigate Drug Design, Drug Discovery, Drug Metabolism and Prediction Via Drug–Drug Interactions
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LigDockTailor: Ligand-specific docking tool matching using multidimensional descriptors
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Computational evaluation of protein–small molecule binding
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Integrated Approach Including Docking, MD Simulations, and Network Analysis Highlights the Action Mechanism of the Cardiac hERG Activator RPR260243
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Sublimation Entropy and Dissociation Constants Prediction by Quantitative Evaluation of Molecular Mobility in Crystals
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PHOENIX: A Scoring Function for Affinity Prediction Derived Using High-Resolution Crystal Structures and Calorimetry Measurements
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An Automated Docking Protocol for hERG Channel Blockers
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Virtual Fragment Screening: Discovery of Histamine H3 Receptor Ligands Using Ligand-Based and Protein-Based Molecular Fingerprints
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inferred← citeshttps://doi.org/10.1021/ci500028uopenalex-snapshot
Improvement of Virtual Screening Results by Docking Data Feature Analysis
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Comparative Assessment of Scoring Functions on a Diverse Test Set
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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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Single-Molecule Pulling Simulations Can Discern Active from Inactive Enzyme Inhibitors
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Improving docking and virtual screening performance using AlphaFold2 multi-state modeling for kinases
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Automatic modeling of mammalian olfactory receptors and docking of odorants
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Applying multi-state modeling using AlphaFold2 for kinases and its application for ensemble screening
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A novel strategy for the structure-based drug design of heat shock protein 90 inhibitors
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Calculation of mobility and entropy of the binding of molecules by crystals
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Evaluation of the Accuracy of Calculation of the Standard Binding Entropy of Molecules from their Average Mobility in Molecular Crystals
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Protein-Ligand Docking in the New Millennium – A Retrospective of 10 Years in the Field
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Calculation of Crystal-Solution Dissociation Constants
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Advances and Challenges in Protein-Ligand Docking
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New Computational Methods to Calculate Drug-Receptor Binding Free Energies
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Scoring Functions of Protein-Ligand Interactions
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Computational investigation of the Plasmodium falciparum fatty acid biosynthetic pathway toward the discovery of novel antimalarials
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ОЦЕНКА ТОЧНОСТИ РАСЧЕТА СТАНДАРТНОЙ ЭНТРОПИИ СВЯЗЫВАНИЯ МОЛЕКУЛ ПО ИХ СРЕДНЕЙ ПОДВИЖНОСТИ В МОЛЕКУЛЯРНЫХ КРИСТАЛЛАХ, "Молекулярная биология"
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Examination of Molecular Recognition in Protein-Ligand Interactions
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