Variability in docking success rates due to dataset preparation.
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The results of cognate docking with the prepared Astex dataset provided by the organizers of the "Docking and Scoring: A Review of Docking Programs" session at the 241st ACS national meeting are presented. The MOE software with the newly developed GBVI/WSA dG scoring function is used throughout the study. For 80 % of the Astex targets, the MOE docker produces a top-scoring pose within 2 Å of the X-ray structure. For 91 % of the targets a pose within 2 Å of the X-ray structure is produced in the top 30 poses. Docking failures, defined as cases where the top scoring pose is greater than 2 Å from the experimental structure, are shown to be largely due to the absence of bound waters in the source dataset, highlighting the need to include these and other crucial information in future standardized sets. Docking success is shown to depend heavily on data preparation. A "dataset preparation" error of 0.5 kcal/mol is shown to cause fluctuations of over 20 % in docking success rates.
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Current docking methods and associated scoring functions exhibit good pose prediction power if the system is adequately prepared and target flexibility does not play a significant role.
“Current docking methods and the associated scoring functions exhibit good pose prediction power if one assumes an adequate preparation of the system and if the target flexibility does not play a significant role (Corbeil et al., 2012; Chaput and Mouawad, 2017).”
From Empirical scoring functions for structure-based virtual screening: applications, critical aspects, and challenges (2018) · cites this paper as Corbeil et al., 2012
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“There are by now multiple widely used and effective docking programs 23 – 31 , employing different strategies for sampling ligand orientations and ligand conformations in the protein site, for handling protein fl exibility, and for scoring ligand fi t once they have been docked.”
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- Authors
- Corbeil, C. R., Williams, C. I., & Labute, P.
- Corresponding author
- Corbeil, Christopher R.
- Venue
- Journal of Computer-Aided Molecular Design
- Published
- 2012-05-08
- Volume
- 26
- Issue
- 6
- Pages
- 775-786
- ISSN
- 0920-654X (ISSN-L)
- 1573-4951
- PMC
- PMC3397132
- OpenAlex
- W2079159737
- Cited by
- 469
- References
- 65
- Citations by year
- 2026: 31 · 2025: 29 · 2024: 40 · 2023: 59 · 2022: 44 · 2021: 46 · 2020: 48 · 2019: 35 · 2018: 32 · 2017: 21 · 2016: 25 · 2015: 25 · 2014: 13 · 2013: 17 · 2012: 4
- FWCI
- 20.61
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- cc-by
- Locations
- Journal of Computer-Aided Molecular Design (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Funders
- GlaxoSmithKline
- Astex Pharmaceuticals
- 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
- Physical Sciences › Physics and Astronomy › Atomic and Molecular Physics, and Optics › Advanced Chemical Physics Studies
- Keywords
- molecular docking, data preparation, bound water, ligand binding free energy, X-ray structure comparison
- MeSH terms
- Algorithms, Binding Sites, Computer Simulation, Hydrogen Bonding, Ligands, Models, Molecular, Protein Binding, Protein Conformation, Proteins, Software, Crystallography, X-Ray
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