The DOI matches its Crossref record; 44 of the 44 references it cites were found in a registry or an index.
Comparison of Topological, Shape, and Docking Methods in Virtual Screening
Abstract
Virtual screening benchmarking studies were carried out on 11 targets to evaluate the performance of three commonly used approaches: 2D ligand similarity (Daylight, TOPOSIM), 3D ligand similarity (SQW, ROCS), and protein structure-based docking (FLOG, FRED, Glide). Active and decoy compound sets were assembled from both the MDDR and the Merck compound databases. Averaged over multiple targets, ligand-based methods outperformed docking algorithms. This was true for 3D ligand-based methods only when chemical typing was included. Using mean enrichment factor as a performance metric, Glide appears to be the best docking method among the three with FRED a close second. Results for all virtual screening methods are database dependent and can vary greatly for particular targets.
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A Critical Assessment of Docking Programs and Scoring Functions
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Comparison of Shape-Matching and Docking as Virtual Screening Tools
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Self-citationDo Structurally Similar Molecules Have Similar Biological Activity?
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Ekins, S., Puhl, A. C., Zorn, K. M., Lane, T. R., Russo, D. P., Klein, J. J., Hickey, A. J., & Clark, A. M. (2019) · Nature Materials · doi:10.1038/s41563-019-0338-z · Cited by 578
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
Recognizing Pitfalls in Virtual Screening: A Critical Review
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Sastry, M., Lowrie, J. F., Dixon, S. L., & Sherman, W. (2010) · Journal of Chemical Information and Modeling · doi:10.1021/ci100062n · Cited by 332
Docking Challenge: Protein Sampling and Molecular Docking Performance
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The discovery of novel HDAC3 inhibitors via virtual screening and in vitro bioassay
Xia, J., Hu, H., Xue, W., Wang, X. S., & Wu, S. (2018) · Journal of Enzyme Inhibition and Medicinal Chemistry · doi:10.1080/14756366.2018.1437156 · Cited by 24
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
Protein-inhibitor interaction studies using NMR
Ishima, R. (2015) · Applications of NMR Spectroscopy · doi:10.2174/9781608059621115010007 · Cited by 13
Metadata
- Authors
- McGaughey, G. B., Sheridan, R. P., Bayly, C. I., Culberson, J. C., Kreatsoulas, C., Lindsley, S., Maiorov, V., Truchon, J.-F., & Cornell, W. D.
- Venue
- Journal of Chemical Information and Modeling
- Publisher
- American Chemical Society (ACS)
- Published
- 2007-06-26
- Volume
- 47
- Issue
- 4
- Pages
- 1504-1519
- ISSN
- 1549-9596 (ISSN-L)
- 1549-960X
- OpenAlex
- W2125792789
- Cited by
- 417
- References
- 44
- FWCI
- 35.02
- Type
- journal article
- Language
- en
- Open access
- closed
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