CSAR benchmark exercise 2011–2012: evaluation of results from docking and relative ranking of blinded congeneric series.
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The Community Structure-Activity Resource (CSAR) recently held its first blinded exercise based on data provided by Abbott, Vertex, and colleagues at the University of Michigan, Ann Arbor. A total of 20 research groups submitted results for the benchmark exercise where the goal was to compare different improvements for pose prediction, enrichment, and relative ranking of congeneric series of compounds. The exercise was built around blinded high-quality experimental data from four protein targets: LpxC, Urokinase, Chk1, and Erk2. Pose prediction proved to be the most straightforward task, and most methods were able to successfully reproduce binding poses when the crystal structure employed was co-crystallized with a ligand from the same chemical series. Multiple evaluation metrics were examined, and we found that RMSD and native contact metrics together provide a robust evaluation of the predicted poses. It was notable that most scoring functions underpredicted contacts between the hetero atoms (i.e., N, O, S, etc.) of the protein and ligand. Relative ranking was found to be the most difficult area for the methods, but many of the scoring functions were able to properly identify Urokinase actives from the inactives in the series. Lastly, we found that minimizing the protein and correcting histidine tautomeric states positively trended with low RMSD for pose prediction but minimizing the ligand negatively trended. Pregenerated ligand conformations performed better than those that were generated on the fly. Optimizing docking parameters and pretraining with the native ligand had a positive effect on the docking performance as did using restraints, substructure fitting, and shape fitting. Lastly, for both sampling and ranking scoring functions, the use of the empirical scoring function appeared to trend positively with the RMSD. Here, by combining the results of many methods, we hope to provide a statistically relevant evaluation and elucidate specific shortcomings of docking methodology for the community.
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Detection of active compounds among decoys and accurate prediction of binding affinity remain challenging tasks, even when induced fit and entropy effects are not important for binding.
“However, the detection of active compounds among a set of decoy compounds and the accurate prediction of binding affinity remain challenging tasks, even when induced fit and entropy effects are not important for binding (Gohlke and Klebe, 2002; Damm-Ganamet et al., 2013; Yuriev and Ramsland, 2013; Grinter and Zou, 2014; Smith et al., 2016).”
From Empirical scoring functions for structure-based virtual screening: applications, critical aspects, and challenges (2018) · cites this paper as Damm-Ganamet et al., 2013
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“…to assess how well participants could model receptor–ligand complexes—a symmetry-corrected r.m.s.d. to measure the absolute accuracy of the predicted ligand within the binding site—and contact-based scores to evaluate the reproduction of native receptor–ligand noncovalent interactions 13,42,43 .”
- Authors
- Damm-Ganamet, K. L., Smith, R. D., Dunbar, J. B., Stuckey, J. A., & Carlson, H. A.
- Affiliations
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1065, United States
- University of Michigan (US)
- Corresponding author
- Carlson, Heather A.
- Venue
- Journal of Chemical Information and Modeling
- Publisher
- American Chemical Society (ACS)
- Published
- 2013-05-10
- Volume
- 53
- Issue
- 8
- Pages
- 1853-1870
- ISSN
- 1549-9596 (ISSN-L)
- 1549-960X
- PMC
- PMC3753884
- OpenAlex
- W2028609644
- Cited by
- 133
- References
- 64
- Citations by year
- 2026: 5 · 2025: 4 · 2024: 5 · 2023: 6 · 2022: 4 · 2021: 7 · 2020: 8 · 2019: 8 · 2018: 10 · 2017: 19 · 2016: 14 · 2015: 24 · 2014: 13 · 2013: 6
- FWCI
- 20.77
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Journal of Chemical Information and Modeling (publishedVersion, other-oa)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institute of General Medical Sciences (U01GM086873)
- 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 › vaccines and immunoinformatics approaches
- Keywords
- molecular docking, benchmark exercise, congeneric series, relative ranking, scoring functions, pose prediction, protein-ligand docking, RMSD, urokinase, LpxC, Chk1, ERK2, protein-ligand binding, ligand conformation, empirical scoring function, structure-activity relationship
- MeSH terms
- Ligands, Protein Conformation, Proteins, Structure-Activity Relationship, Drug Design, Benchmarking, Molecular Docking Simulation, Databases, Pharmaceutical
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