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Development and validation of a genetic algorithm for flexible docking 1 1Edited by F. E. Cohen
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 (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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Ying, Y., Yao, K., Repasky, M. P., Leswing, K., Abel, R., Shoichet, B. K., & Jerome, S. V. (2021) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.1c00810 · Cited by 480
Perola, E., & Charifson, P. S. (2004) · Journal of Medicinal Chemistry · doi:10.1021/jm030563w · Cited by 452
Prediction of protein–protein interactions by docking methods
Smith, G. R., & Sternberg, M. J. E. (2002) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(02)00285-3 · Cited by 450
A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance
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Metadata
- 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
- Venue
- Journal of Molecular Biology
- Publisher
- Elsevier BV
- Published
- 1997-04
- Volume
- 267
- Issue
- 3
- Pages
- 727-748
- ISSN
- 0022-2836 (ISSN-L)
- 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
- Locations
- Journal of Molecular Biology (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Pharmacology, Toxicology and Pharmaceutics › Drug Discovery › 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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