The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
FRED Pose Prediction and Virtual Screening Accuracy
Abstract
Results of a previous docking study are reanalyzed and extended to include results from the docking program FRED and a detailed statistical analysis of both structure reproduction and virtual screening results. FRED is run both in a traditional docking mode and in a hybrid mode that makes use of the structure of a bound ligand in addition to the protein structure to screen molecules. This analysis shows that most docking programs are effective overall but highly inconsistent, tending to do well on one system and poorly on the next. Comparing methods, the difference in mean performance on DUD is found to be statistically significant (95% confidence) 61% of the time when using a global enrichment metric (AUC). Early enrichment metrics are found to have relatively poor statistical power, with 0.5% early enrichment only able to distinguish methods to 95% confidence 14% of the time.
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Cites
Benchmarking sets for molecular docking.
Huang, N., Shoichet, B. K., & Irwin, J. J. (2006) · Journal of Medicinal Chemistry · doi:10.1021/jm0608356 · Cited by 1,318
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Key Topics in Molecular Docking for Drug Design
Torres, P. H. M., Sodero, A. C. R., Jofily, P., & Silva-Jr, F. P. (2019) · International Journal of Molecular Sciences · doi:10.3390/ijms20184574 · Cited by 641
Chen, Y.-C. (2015) · Trends in Pharmacological Sciences · doi:10.1016/j.tips.2014.12.001 · Cited by 611
A practical guide to large-scale docking
Bender, B. J., Gahbauer, S., Luttens, A., Lyu, J., Webb, C. M., Stein, R. M., Fink, E. A., Balius, T. E., Carlsson, J., Irwin, J. J., et al. (2021) · Nature Protocols · doi:10.1038/s41596-021-00597-z · Cited by 546
Gentile, F., Yaacoub, J. C., Gleave, J., Fernandez, M., Ton, A.-T., Ban, F., Stern, A., & Cherkasov, A. (2022) · Nature Protocols · doi:10.1038/s41596-021-00659-2 · Cited by 397
Metadata
- Authors
- McGann, M.
- Venue
- Journal of Chemical Information and Modeling
- Publisher
- American Chemical Society (ACS)
- Published
- 2011-02-16
- Volume
- 51
- Issue
- 3
- Pages
- 578-596
- ISSN
- 1549-9596 (ISSN-L)
- 1549-960X
- OpenAlex
- W2061583504
- Cited by
- 764
- References
- 1
- FWCI
- 29.60
- Type
- journal article
- Language
- en
- Open access
- closed
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
