The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
Comparative Performance of Several Flexible Docking Programs and Scoring Functions: Enrichment Studies for a Diverse Set of Pharmaceutically Relevant Targets
Open accessAbstract
Virtual screening by molecular docking has become a widely used approach to lead discovery in the pharmaceutical industry when a high-resolution structure of the biological target of interest is available. The performance of three widely used docking programs (Glide, GOLD, and DOCK) for virtual database screening is studied when they are applied to the same protein target and ligand set. Comparisons of the docking programs and scoring functions using a large and diverse data set of pharmaceutically interesting targets and active compounds are carried out. We focus on the problem of docking and scoring flexible compounds which are sterically capable of docking into a rigid conformation of the receptor. The Glide XP methodology is shown to consistently yield enrichments superior to the two alternative methods, while GOLD outperforms DOCK on average. The study also shows that docking into multiple receptor structures can decrease the docking error in screening a diverse set of active compounds.
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Cites
Friesner, R. A., Banks, J. L., Murphy, R. B., Halgren, T. A., Klicic, J. J., Mainz, D. T., Repasky, M. P., Knoll, E. H., Shelley, M., Perry, J. K., et al. (2004) · Journal of Medicinal Chemistry · doi:10.1021/jm0306430 · Cited by 10,057
Self-citationDevelopment and validation of a genetic algorithm for flexible docking 1 1Edited by F. E. Cohen
Jones, G., Willett, P., Glen, R. C., Leach, A. R., & Taylor, R. (1997) · Journal of Molecular Biology · doi:10.1006/jmbi.1996.0897 · Cited by 6,763
Comparative evaluation of 11 scoring functions for molecular docking.
Wang, R., Lu, Y., & Wang, S. (2003) · Journal of Medicinal Chemistry · doi:10.1021/jm0203783 · Cited by 849
Cited by
Improved Docking of Polypeptides with Glide
Tubert-Brohman, I., Sherman, W., Repasky, M., & Beuming, T. (2013) · Journal of Chemical Information and Modeling · doi:10.1021/ci400128m · Cited by 1,308
Efficient Drug Lead Discovery and Optimization
Jorgensen, W. L. (2009) · Accounts of Chemical Research · doi:10.1021/ar800236t · Cited by 649
Moitessier, N., Englebienne, P., Lee, D., Lawandi, J., & Corbeil, C. R. (2008) · British Journal of Pharmacology · doi:10.1038/sj.bjp.0707515 · Cited by 514
Ban, F., Dalal, K., Li, H., LeBlanc, E., Rennie, P. S., & Cherkasov, A. (2017) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.7b00137 · Cited by 109
Nagaraju, M., McGowan, L. C., & Hamelberg, D. (2013) · Journal of Chemical Information and Modeling · doi:10.1021/ci300432w · Cited by 18
Metadata
- Authors
- Zhou, Z., Felts, A. K., Friesner, R. A., & Levy, R. M.
- Venue
- Journal of Chemical Information and Modeling
- Publisher
- American Chemical Society (ACS)
- Published
- 2007-06-23
- Volume
- 47
- Issue
- 4
- Pages
- 1599-1608
- ISSN
- 1549-9596 (ISSN-L)
- 1549-960X
- OpenAlex
- W2112101018
- Cited by
- 165
- References
- 3
- FWCI
- 17.51
- Type
- journal article
- Language
- en
- Open access
- green
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