POVME: An algorithm for measuring binding-pocket volumes

被引：182

作者：

Durrant, Jacob D. ^{[1
]}

de Oliveira, Cesar Augusto F. ^{[2
,3
,4
]}

McCammon, J. Andrew ^{[2
,3
,4
]}

机构：

[1] Univ Calif San Diego, Dept Chem & Biochem, La Jolla, CA 92093 USA

[2] Univ Calif San Diego, Howard Hughes Med Inst, La Jolla, CA 92093 USA

[3] Univ Calif San Diego, Dept Chem & Biochem, Dept Pharmacol, La Jolla, CA 92093 USA

[4] Univ Calif San Diego, NSF Ctr Theoret Biol Phys, La Jolla, CA 92093 USA

来源：

JOURNAL OF MOLECULAR GRAPHICS & MODELLING | 2011年 / 29卷 / 05期

关键词：

POVME; Binding-pocket volume; Algorithm; Computer-aided drug design; MATRIX-METALLOPROTEINASE INHIBITORS; STROMELYSIN CATALYTIC DOMAIN; X-RAY-STRUCTURE;

D O I：

10.1016/j.jmgm.2010.10.007

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：773 / 776

页数：4

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