Recognizing protein-protein interfaces with empirical potentials and reduced amino acid alphabets.

ABSTRACT:

Background

In structural genomics, an important goal is the detection and classification of protein-protein interactions, given the structures of the interacting partners. We have developed empirical energy functions to identify native structures of protein-protein complexes among sets of decoy structures. To understand the role of amino acid diversity, we parameterized a series of functions, using a hierarchy of amino acid alphabets of increasing complexity, with 2, 3, 4, 6, and 20 amino acid groups. Compared to previous work, we used the simplest possible functional form, with residue-residue interactions and a stepwise distance-dependence. We used increased computational resources, however, constructing 290,000 decoys for 219 protein-protein complexes, with a realistic docking p

SUBMITTER: Launay G 

PROVIDER: S-EPMC2034607 | biostudies-literature | 2007 Jul

REPOSITORIES: biostudies-literature