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Functionality maps of binding sites: A multiple copy simultaneous search method
Abstract
A new method is proposed for determining energetically favorable positions and orientations for functional groups on the surface of proteins with known three‐dimensional structure. From 1,000 to 5,000 copies of a functional group are randomly placed in the site and subjected to simultaneous energy minimization and/or quenched molecular dynamics. The resulting functionality maps of a protein receptor site, which can take account of its flexibility, can be used for the analysis of protein ligand interactions and rational drug design. Application of the method to the sialic acid binding site of the influenza coat protein, hemagglutinin, yields functional group minima that correspond with those of the ligand in a cocrystal structure.
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Cited by
Molecular Docking: A Powerful Approach for Structure-Based Drug Discovery
Meng, X.-Y., Zhang, H.-X., Mezei, M., & Cui, M. (2011) · Current Computer Aided-Drug Design · doi:10.2174/157340911795677602 · Cited by 3,771
Software for molecular docking: a review
Pagadala, N. S., Syed, K., & Tuszynski, J. (2017) · Biophysical Reviews · doi:10.1007/s12551-016-0247-1 · Cited by 1,522
Principles of docking: An overview of search algorithms and a guide to scoring functions
Halperin, I., Ma, B., Wolfson, H., & Nussinov, R. (2002) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.10115 · Cited by 1,294
The Process of Structure-Based Drug Design
Anderson, A. C. (2003) · Chemistry & Biology · doi:10.1016/j.chembiol.2003.09.002 · Cited by 939
Brenke, R., Kozakov, D., Chuang, G.-Y., Beglov, D., Hall, D., Landon, M. R., Mattos, C., & Vajda, S. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp036 · Cited by 455
Metadata
- Authors
- Miranker, A., & Karplus, M.
- Venue
- Proteins: Structure, Function, and Bioinformatics
- Publisher
- Wiley
- Published
- 1991-09
- Volume
- 11
- Issue
- 1
- Pages
- 29-34
- ISSN
- 0887-3585 (ISSN-L)
- 1097-0134
- OpenAlex
- W2064514012
- Cited by
- 544
- References
- 0
- FWCI
- 14.65
- Type
- journal article
- Language
- en
- Open access
- closed
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- Miranker, A., & Karplus, M. (1991). Functionality maps of binding sites: A multiple copy simultaneous search method. Proteins: Structure, Function, and Bioinformatics. https://doi.org/10.1002/prot.340110104
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