A simple contact mapping algorithm for identifying potential peptide mimetics in protein-protein interaction partners.

ABSTRACT: A simple, static contact mapping algorithm has been developed as a first step at identifying potential peptide biomimetics from protein interaction partner structure files. This rapid and simple mapping algorithm, "OpenContact" provides screened or parsed protein interaction files based on specified criteria for interatomic separation distances and interatomic potential interactions. The algorithm, which uses all-atom Amber03 force field models, was blindly tested on several unrelated cases from the literature where potential peptide mimetics have been experimentally developed to varying degrees of success. In all cases, the screening algorithm efficiently predicted proposed or potential peptide biomimetics, or close variations thereof, and provided complete atom-atom interaction data nece

SUBMITTER: Krall A 

PROVIDER: S-EPMC4369124 | biostudies-literature | 2014 Sep

REPOSITORIES: biostudies-literature