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

Jones, Gareth; Willett, Peter; Glen, Robert C; Leach, Andrew R; Taylor, Robin

doi:10.1006/jmbi.1996.0897

Cited by 6,763Computational Drug Discovery MethodsProtein Structure and DynamicsProtein Interaction Studies and Fluorescence Analysis

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

Jones, Gareth, Willett, Peter, Glen, Robert C, Leach, Andrew R, Taylor, Robin·1997·Journal of Molecular Biology

DOI 10.1006/jmbi.1996.0897

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Abstract

Prediction of small molecule binding modes to macromolecules of known three-dimensional structure is a problem of paramount importance in rational drug design (the "docking" problem). We report the development and validation of the program GOLD (Genetic Optimisation for Ligand Docking). GOLD is an automated ligand docking program that uses a genetic algorithm to explore the full range of ligand conformational flexibility with partial flexibility of the protein, and satisfies the fundamental requirement that the ligand must displace loosely bound water on binding. Numerous enhancements and modifications have been applied to the original technique resulting in a substantial increase in the reliability and the applicability of the algorithm. The advanced algorithm has been tested on a dataset of 100 complexes extracted from the Brookhaven Protein DataBank. When used to dock the ligand back into the binding site, GOLD achieved a 71% success rate in identifying the experimental binding mode.

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GOLD, Autodock4, CovalentDock, CovDock, DOCKovalent, and DOCK-TITE are examples of docking programs that developed specific methodologies to deal with covalent docking.
“GOLD (Jones et al., 1997), Autodock4 (Bianco et al., 2016), CovalentDock (Ouyang et al., 2013), CovDock (Zhu et al., 2014), DOCKovalent (London et al., 2014), and DOCK-TITE (Scholz et al., 2015) are some examples of docking programs that developed specific methodologies to deal with covalent-docking.”
From Empirical scoring functions for structure-based virtual screening: applications, critical aspects, and challenges (2018) · cites this paper as Jones et al., 1997

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Authors: Jones, G., Willett, P., Glen, R. C., Leach, A. R., & Taylor, R.
Affiliations: University of Sheffield (GB)
Wellcome Trust (GB)
Cambridge Crystallographic Data Centre (GB)
Corresponding author: Jones, Gareth
ORCID: Jones, Gareth
Willett, Peter
Glen, Robert C
Leach, Andrew R
Taylor, Robin
Venue: Journal of Molecular Biology
Publisher: Elsevier BV
Published: 1997-04
Volume: 267
Issue: 3
Pages: 727-748
ISSN: 0022-2836 (ISSN-L)
DOI: 10.1006/jmbi.1996.0897
OpenAlex: W2050456292
Cited by: 6,763
References: 87
Citations by year: 2026: 244 · 2025: 332 · 2024: 356 · 2023: 361 · 2022: 383 · 2021: 414 · 2020: 394 · 2019: 351 · 2018: 327 · 2017: 270 · 2016: 248 · 2015: 234 · 2014: 237 · 2013: 248 · 2012: 274
Type: book review
Language: en
Open access: closed
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
Locations: Journal of Molecular Biology (publishedVersion)
PubMed (publishedVersion)
Topics: Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Interaction Studies and Fluorescence Analysis
Keywords: protein-ligand docking, genetic algorithm, flexible docking, protein-ligand complex, ligand conformational flexibility, rational drug design, binding mode prediction
MeSH terms: Algorithms, Binding Sites, Computer Simulation, Humans, Ligands, Models, Genetic, Models, Molecular, NADP, Protein Binding, Protein Conformation, Proteins, Tetrahydrofolate Dehydrogenase, Crystallography, X-Ray

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