A library of protein surface patches discriminates between native structures and decoys generated by structure prediction servers.

ABSTRACT:

Background

Protein surfaces serve as an interface with the molecular environment and are thus tightly bound to protein function. On the surface, geometric and chemical complementarity to other molecules provides interaction specificity for ligand binding, docking of bio-macromolecules, and enzymatic catalysis.As of today, there is no accepted general scheme to represent protein surfaces. Furthermore, most of the research on protein surface focuses on regions of specific interest such as interaction, ligand binding, and docking sites. We present a first step toward a general purpose representation of protein surfaces: a novel surface patch library that represents most surface patches (~98%) in a data set regardless of their functional roles.

Results

Surface patches, in this w

SUBMITTER: Gamliel R 

PROVIDER: S-EPMC3114701 | biostudies-literature | 2011 May

REPOSITORIES: biostudies-literature