Contact prediction for beta and alpha-beta proteins using integer linear optimization and its impact on the first principles 3D structure prediction method ASTRO-FOLD.

ABSTRACT: An integer linear optimization model is presented to predict residue contacts in beta, alpha + beta, and alpha/beta proteins. The total energy of a protein is expressed as sum of a C(alpha)-C(alpha) distance dependent contact energy contribution and a hydrophobic contribution. The model selects contact that assign lowest energy to the protein structure as satisfying a set of constraints that are included to enforce certain physically observed topological information. A new method based on hydrophobicity is proposed to find the beta-sheet alignments. These beta-sheet alignments are used as constraints for contacts between residues of beta-sheets. This model was tested on three independent protein test sets and CASP8 test proteins consisting of beta, alpha + beta, alpha/beta proteins and it

SUBMITTER: Rajgaria R 

PROVIDER: S-EPMC2858251 | biostudies-literature | 2010 Jun

REPOSITORIES: biostudies-literature