An algorithm for predicting protein-protein interaction sites: Abnormally exposed amino acid residues and secondary structure elements.

ABSTRACT: Multiprotein systems mediate most regulatory processes in living organisms. Although the structures of the individual proteins are often defined, less is known of the structures of multiprotein systems. Computational methods for predicting interfaces, using evolutionary conservation and/or physicochemical data, have been developed. Here we consider the use of solvent accessibility, residue propensity, and hydrophobicity, in conjunction with secondary structure data, as prediction parameters. We analyze the influence of residue type and secondary structure on solvent accessibility and define a measure of "relative exposedness." Clustering abnormally high scoring residues provides a basis for predicting interaction sites. The analysis is extended to investigate abnormally exposed secondary s

SUBMITTER: Hoskins J 

PROVIDER: S-EPMC2242518 | biostudies-literature | 2006 May

REPOSITORIES: biostudies-literature