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Novel statistical‐thermodynamic methods to predict protein‐ligand binding positions using probability distribution functions
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1002/(sici)1096-987x(19981115)19:14<1639::aid-jcc10>3.0.co;2-bopenalex-snapshot
Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
inferredcites →https://doi.org/10.1002/(sici)1097-0134(199706)28:2<144::aid-prot2>3.0.co;2-fopenalex-snapshot
Loss of translational entropy in binding, folding, and catalysis
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Approaches to the Description and Prediction of the Binding Affinity of Small-Molecule Ligands to Macromolecular Receptors
inferredcites →https://doi.org/10.1002/jcc.20082openalex-snapshot
Empirical force fields for biological macromolecules: Overview and issues
inferredcites →https://doi.org/10.1002/jcc.20246openalex-snapshot
New and fast statistical‐thermodynamic method for computation of protein‐ligand binding entropy substantially improves docking accuracy
inferredcites →https://doi.org/10.1002/prot.10115openalex-snapshot
Principles of docking: An overview of search algorithms and a guide to scoring functions
inferredcites →https://doi.org/10.1002/prot.10394openalex-snapshot
Successful discrimination of protein interactions
inferredcites →https://doi.org/10.1002/prot.1170openalex-snapshot
Rosetta in CASP4: Progress in ab initio protein structure prediction
inferredcites →https://doi.org/10.1002/prot.20149openalex-snapshot
Comparative evaluation of eight docking tools for docking and virtual screening accuracy
inferredcites →https://doi.org/10.1002/prot.20385openalex-snapshot
The key role of atom types, reference states, and interaction cutoff radii in the knowledge‐based method: New variational approach
inferredcites →https://doi.org/10.1016/s1074-5521(97)90251-9openalex-snapshot
A new class of models for computing receptor-ligand binding affinities
inferredcites →https://doi.org/10.1021/ja963568+openalex-snapshot
Inclusion of Loss of Translational and Rotational Freedom in Theoretical Estimates of Free Energies of Binding. Application to a Complex of Benzene and Mutant T4 Lysozyme
inferredcites →https://doi.org/10.1021/jm00026a001openalex-snapshot
Computational Methods to Predict Binding Free Energy in Ligand-Receptor Complexes
inferredcites →https://doi.org/10.1021/jm0003992openalex-snapshot
Detailed Analysis of Scoring Functions for Virtual Screening
inferredcites →https://doi.org/10.1021/jm001044lopenalex-snapshot
Protein-Based Virtual Screening of Chemical Databases. 1. Evaluation of Different Docking/Scoring Combinations
inferredcites →https://doi.org/10.1021/jm0101141openalex-snapshot
Hierarchy of Simulation Models in Predicting Structure and Energetics of the Src SH2 Domain Binding to Tyrosyl Phosphopeptides
inferredcites →https://doi.org/10.1021/jm010141ropenalex-snapshot
Evaluation of Docking Functions for Protein−Ligand Docking
inferredcites →https://doi.org/10.1021/jm0203783openalex-snapshot
Comparative Evaluation of 11 Scoring Functions for Molecular Docking
inferredcites →https://doi.org/10.1021/jm0302997openalex-snapshot
Evaluation of Docking Performance: Comparative Data on Docking Algorithms
inferredcites →https://doi.org/10.1021/jm0498147openalex-snapshot
Assessment of Multiple Binding Modes in Ligand−Protein Docking
inferredcites →https://doi.org/10.1023/a:1020155510718openalex-snapshot
A review of protein-small molecule docking methods
inferredcites →https://doi.org/10.1023/b:jcam.0000004604.87558.02openalex-snapshot
Automated docking of ligands to an artificial active site: augmenting crystallographic analysis with computer modeling
inferredcites →https://doi.org/10.1038/nature03196openalex-snapshot
Exploring biology with small organic molecules
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Virtual screening of chemical libraries
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A “fast growth” method of computing free energy differences
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Computational mapping identifies the binding sites of organic solvents on proteins
inferredcites →https://doi.org/10.1073/pnas.102179699openalex-snapshot
Evaluating conformational free energies: The colony energy and its application to the problem of loop prediction
inferredcites →https://doi.org/10.1073/pnas.95.19.11158openalex-snapshot
Clustering of low-energy conformations near the native structures of small proteins
inferredcites →https://doi.org/10.1093/protein/3.1.1openalex-snapshot
The price of lost freedom: entropy of bimolecular complex formation
inferredcites →https://doi.org/10.1146/annurev.biophys.30.1.211openalex-snapshot
Biomolecular Simulations: Recent Developments in Force Fields, Simulations of Enzyme Catalysis, Protein-Ligand, Protein-Protein, and Protein-Nucleic Acid Noncovalent Interactions
inferredcites →https://doi.org/10.1146/annurev.biophys.32.110601.142532openalex-snapshot
Molecular Recognition and Docking Algorithms
inferredcites →https://doi.org/10.1186/1472-6807-4-1openalex-snapshot
Consensus structural models for the amino terminal domain of the retrovirus restriction gene Fv1 and the Murine Leukaemia Virus capsid proteins
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1002/jcc.20580openalex-snapshot
Role of binding entropy in the refinement of protein–ligand docking predictions: Analysis based on the use of 11 scoring functions
inferred← citeshttps://doi.org/10.1002/jcc.20936openalex-snapshot
Empirical entropic contributions in computational docking: Evaluation in APS reductase complexes
inferred← citeshttps://doi.org/10.1002/prot.21844openalex-snapshot
A statistical rescoring scheme for protein–ligand docking: Consideration of entropic effect
inferred← citeshttps://doi.org/10.1002/prot.21997openalex-snapshot
Discrimination of near‐native structures in protein–protein docking by testing the stability of local minima
inferred← citeshttps://doi.org/10.1002/prot.24103openalex-snapshot
Rotamer libraries and probabilities of transition between rotamers for the side chains in protein–protein binding
inferred← citeshttps://doi.org/10.1007/978-1-4939-7899-1_12openalex-snapshot
Approaching Pharmacological Space: Events and Components
inferred← citeshttps://doi.org/10.1007/s10822-007-9116-0openalex-snapshot
Calculations of protein-ligand binding entropy of relative and overall molecular motions
inferred← citeshttps://doi.org/10.1007/s10822-009-9283-2openalex-snapshot
Detection of ligand binding hot spots on protein surfaces via fragment-based methods: application to DJ-1 and glucocerebrosidase
inferred← citeshttps://doi.org/10.1007/s10822-010-9356-2openalex-snapshot
Chemical space sampling by different scoring functions and crystal structures
inferred← citeshttps://doi.org/10.1007/s10822-017-0053-2openalex-snapshot
Performance of multiple docking and refinement methods in the pose prediction D3R prospective Grand Challenge 2016
inferred← citeshttps://doi.org/10.1007/s12539-012-0046-8openalex-snapshot
Computer based screening for novel inhibitors against Vibrio cholerae using NCI diversity set-II: An alternative approach by targeting transcriptional activator ToxT
inferred← citeshttps://doi.org/10.1016/j.compbiolchem.2018.03.027openalex-snapshot
A vibrational entropy term for DNA docking with autodock
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c00596openalex-snapshot
Integrated Approach Including Docking, MD Simulations, and Network Analysis Highlights the Action Mechanism of the Cardiac hERG Activator RPR260243
inferred← citeshttps://doi.org/10.1021/acs.jcim.6b00373openalex-snapshot
Efficient Approximation of Ligand Rotational and Translational Entropy Changes upon Binding for Use in MM-PBSA Calculations
inferred← citeshttps://doi.org/10.1039/9781849735377-00171openalex-snapshot
Docking and Virtual Screening
inferred← citeshttps://doi.org/10.1093/bioinformatics/btp036openalex-snapshot
Fragment-based identification of druggable ‘hot spots’ of proteins using Fourier domain correlation techniques
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