The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
How To Optimize Shape-Based Virtual Screening: Choosing the Right Query and Including Chemical Information
Abstract
Shape-based molecular similarity approaches have been established as important and popular virtual screening techniques. Recent applications have shown successful screening campaigns using different parameters and query selection. It is common sense that pure volume overlap scoring (or "shape-based screening") under-represents chemical or pharmacophoric information of a molecule. Using the "Directory of Useful Decoys" (DUD) as a benchmark set, we systematically evaluate how (i) the choice of query conformations, (ii) the selection of the active compound to be used as a query structure, and (iii) the inclusion of chemical information (i.e., the pharmacophoric properties of the query molecule) affect screening performance. Varying these parameters bears remarkable potential for improvements and delivers the best screening performance reported using these tools so far. From these insights, guidelines on how to reach optimum performance during virtual screening are developed.
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Cites
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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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Cited by
Recognizing Pitfalls in Virtual Screening: A Critical Review
Scior, T., Bender, A., Tresadern, G., Medina-Franco, J. L., Martínez-Mayorga, K., Langer, T., Cuanalo-Contreras, K., & Agrafiotis, D. K. (2012) · Journal of Chemical Information and Modeling · doi:10.1021/ci200528d · Cited by 438
Next generation 3D pharmacophore modeling
Schaller, D., Šribar, D., Noonan, T., Deng, L., Nguyen, T. N., Pach, S., Machalz, D., Bermudez, M., & Wolber, G. (2020) · WIREs Computational Molecular Science · doi:10.1002/wcms.1468 · Cited by 269
Self-citationThe effect of ligand-based tautomer and protomer prediction on structure-based virtual screening.
Kalliokoski, T., Salo, H. S., Lahtela-Kakkonen, M., & Poso, A. (2009) · Journal of Chemical Information and Modeling · doi:10.1021/ci900364w · Cited by 66
Kaserer, T., Temml, V., Kutil, Z., Vanek, T., Landa, P., & Schuster, D. (2015) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2015.04.017 · Cited by 23
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Metadata
- Authors
- Kirchmair, J., Distinto, S., Markt, P., Schuster, D., Spitzer, G. M., Liedl, K. R., & Wolber, G.
- Venue
- Journal of Chemical Information and Modeling
- Publisher
- American Chemical Society (ACS)
- Published
- 2009-02-18
- Volume
- 49
- Issue
- 3
- Pages
- 678-692
- ISSN
- 1549-9596 (ISSN-L)
- 1549-960X
- OpenAlex
- W1989856356
- Cited by
- 193
- References
- 3
- FWCI
- 17.38
- Type
- journal article
- Language
- en
- Open access
- closed
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- Kirchmair, J., Distinto, S., Markt, P., Schuster, D., Spitzer, G. M., Liedl, K. R., & Wolber, G. (2009). How To Optimize Shape-Based Virtual Screening: Choosing the Right Query and Including Chemical Information. Journal of Chemical Information and Modeling. https://doi.org/10.1021/ci8004226
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