POVME: an algorithm for measuring binding-pocket volumes.

Authors :: Durrant JD
de Oliveira CA
McCammon JA
Source :: Journal of molecular graphics & modelling [J Mol Graph Model] 2011 Feb; Vol. 29 (5), pp. 773-6. Date of Electronic Publication: 2010 Nov 03.
Publication Year :: 2011
Abstract: 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.<br /> (Copyright © 2010 Elsevier Inc. All rights reserved.)