Localization of binding sites in protein structures by optimization of a composite scoring function.

ABSTRACT: The rise in the number of functionally uncharacterized protein structures is increasing the demand for structure-based methods for functional annotation. Here, we describe a method for predicting the location of a binding site of a given type on a target protein structure. The method begins by constructing a scoring function, followed by a Monte Carlo optimization, to find a good scoring patch on the protein surface. The scoring function is a weighted linear combination of the z-scores of various properties of protein structure and sequence, including amino acid residue conservation, compactness, protrusion, convexity, rigidity, hydrophobicity, and charge density; the weights are calculated from a set of previously identified instances of the binding-site type on known protein structures.

SUBMITTER: Rossi A 

PROVIDER: S-EPMC2242385 | biostudies-literature | 2006 Oct

REPOSITORIES: biostudies-literature