The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
Optimizing Fragment and Scaffold Docking by Use of Molecular Interaction Fingerprints
Abstract
Protein-ligand interaction fingerprints have been used to postprocess docking poses of three ligand data sets: a set of 40 low-molecular-weight compounds from the Protein Data Bank, a collection of 40 scaffolds from pharmaceutically relevant protein ligands, and a database of 19 scaffolds extracted from true cdk2 inhibitors seeded in 2230 scaffold decoys. Four popular docking tools (FlexX, Glide, Gold, and Surflex) were used to generate poses for ligands of the three data sets. In all cases, scoring by the similarity of interaction fingerprints to a given reference was statistically superior to conventional scoring functions in posing low-molecular-weight fragments, predicting protein-bound scaffold coordinates according to the known binding mode of related ligands, and screening a scaffold library to enrich a hit list in true cdk2-targeted scaffolds.
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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
Bissantz, C., Folkers, G., & Rognan, D. (2000) · Journal of Medicinal Chemistry · doi:10.1021/jm001044l · Cited by 740
Self-citationComparative evaluation of eight docking tools for docking and virtual screening accuracy
Kellenberger, E., Rodrigo, J., Muller, P., & Rognan, D. (2004) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.20149 · Cited by 577
Self-citation
Cited by
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
Damm-Ganamet, K. L., Smith, R. D., Dunbar, J. B., Stuckey, J. A., & Carlson, H. A. (2013) · Journal of Chemical Information and Modeling · doi:10.1021/ci400025f · Cited by 133
Fragment Informatics and Computational Fragment‐Based Drug Design: An Overview and Update
Sheng, C., & Zhang, W. (2013) · Medicinal Research Reviews · doi:10.1002/med.21255 · Cited by 80
Ding, B., Wang, J., Li, N., & Wang, W. (2013) · Journal of Chemical Information and Modeling · doi:10.1021/ci300508m · Cited by 45
Harnessing systematic protein–ligand interaction fingerprints for drug discovery
Zhao, Z., & Bourne, P. E. (2022) · Drug Discovery Today · doi:10.1016/j.drudis.2022.07.004 · Cited by 41
Metadata
- Authors
- Marcou, G., & Rognan, D.
- Venue
- Journal of Chemical Information and Modeling
- Publisher
- American Chemical Society (ACS)
- Published
- 2006-12-09
- Volume
- 47
- Issue
- 1
- Pages
- 195-207
- ISSN
- 1549-9596 (ISSN-L)
- 1549-960X
- OpenAlex
- W2168045053
- Cited by
- 408
- References
- 3
- FWCI
- 12.30
- Type
- journal article
- Language
- en
- Open access
- closed
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