Rapid comparison of protein binding site surfaces with property encoded shape distributions.

ABSTRACT: Patterns in shape and property distributions on the surface of binding sites are often conserved across functional proteins without significant conservation of the underlying amino-acid residues. To explore similarities of these sites from the viewpoint of a ligand, a sequence and fold-independent method was created to rapidly and accurately compare binding sites of proteins represented by property-mapped triangulated Gauss-Connolly surfaces. Within this paradigm, signatures for each binding site surface are produced by calculating their property-encoded shape distributions (PESD), a measure of the probability that a particular property will be at a specific distance to another on the molecular surface. Similarity between the signatures can then be treated as a measure of similarity betwee

SUBMITTER: Das S 

PROVIDER: S-EPMC2804948 | biostudies-literature | 2009 Dec

REPOSITORIES: biostudies-literature