Journal
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
Volume 29, Issue 5, Pages 773-776Publisher
ELSEVIER SCIENCE INC
DOI: 10.1016/j.jmgm.2010.10.007
Keywords
POVME; Binding-pocket volume; Algorithm; Computer-aided drug design
Categories
Funding
- NIH [GM31749]
- NSF [MCB-0506593, MCA93S013]
- Howard Hughes Medical Institute
- National Center for Supercomputing Applications
- San Diego Supercomputer Center
- W.M. Keck Foundation
- National Biomedical Computational Resource
- Center for Theoretical Biological Physics
- NSF Supercomputer Centers
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Researchers engaged in computer-aided drug design often wish to measure the volume of a ligand-binding pocket in order to predict pharmacology. We have recently developed a simple algorithm, called POVME (POcket Volume MEasurer), for this purpose. POVME is Python implemented, fast, and freely available. To demonstrate its utility, we use the new algorithm to study three members of the matrix-metalloproteinase family of proteins. Despite the structural similarity of these proteins, differences in binding-pocket dynamics are easily identified. (C) 2010 Elsevier Inc. All rights reserved.
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