APoc: large-scale identification of similar protein pockets.

ABSTRACT:

Motivation

Most proteins interact with small-molecule ligands such as metabolites or drug compounds. Over the past several decades, many of these interactions have been captured in high-resolution atomic structures. From a geometric point of view, most interaction sites for grasping these small-molecule ligands, as revealed in these structures, form concave shapes, or 'pockets', on the protein's surface. An efficient method for comparing these pockets could greatly assist the classification of ligand-binding sites, prediction of protein molecular function and design of novel drug compounds.

Results

We introduce a computational method, APoc (Alignment of Pockets), for the large-scale, sequence order-independent, structural comparison of protein pockets. A scoring function, th

SUBMITTER: Gao M 

PROVIDER: S-EPMC3582269 | biostudies-literature | 2013 Mar

REPOSITORIES: biostudies-literature