VASP: a volumetric analysis of surface properties yields insights into protein-ligand binding specificity.

ABSTRACT: Many algorithms that compare protein structures can reveal similarities that suggest related biological functions, even at great evolutionary distances. Proteins with related function often exhibit differences in binding specificity, but few algorithms identify structural variations that effect specificity. To address this problem, we describe the Volumetric Analysis of Surface Properties (VASP), a novel volumetric analysis tool for the comparison of binding sites in aligned protein structures. VASP uses solid volumes to represent protein shape and the shape of surface cavities, clefts and tunnels that are defined with other methods. Our approach, inspired by techniques from constructive solid geometry, enables the isolation of volumetrically conserved and variable regions within three dim

SUBMITTER: Chen BY 

PROVIDER: S-EPMC2930297 | biostudies-literature | 2010 Aug

REPOSITORIES: biostudies-literature