title: POVME: an algorithm for measuring binding-pocket volumes.
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.
authors.affiliation: Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, CA 92093-0365, USA. jdurrant@ucsd.edu
authors.forename: Jacob D
authors.initials: JD
authors.lastname: Durrant
authors.forename: César Augusto F
authors.initials: CA
authors.lastname: de Oliveira
authors.forename: J Andrew
authors.initials: JA
authors.lastname: McCammon
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D015195:Drug Design; D007527:Isoenzymes / Q000737:chemistry; D020782:Matrix Metalloproteinases / Q000737:chemistry; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*
chemical_list: D007527:Isoenzymes; D011506:Proteins; D020782:Matrix Metalloproteinases