PEP-SiteFinder: a tool for the blind identification of peptide binding sites on protein surfaces.

ABSTRACT: Peptide-protein interactions are important to many processes of life, particularly for signal transmission or regulatory mechanisms. When no information is known about the interaction between a protein and a peptide, it is of interest to propose candidate sites of interaction at the protein surface, to assist the design of biological experiments to probe the interaction, or to serve as a starting point for more focused in silico approaches. PEP-SiteFinder is a tool that will, given the structure of a protein and the sequence of a peptide, identify protein residues predicted to be at peptide-protein interface. PEP-SiteFinder relies on the 3D de novo generation of peptide conformations given its sequence. These conformations then undergo a fast blind rigid docking on the complete protein sur

SUBMITTER: Saladin A 

PROVIDER: S-EPMC4086095 | biostudies-literature | 2014 Jul

REPOSITORIES: biostudies-literature