Docking server for the identification of heparin binding sites on proteins.

ABSTRACT: Many proteins of widely differing functionality and structure are capable of binding heparin and heparan sulfate. Since crystallizing protein-heparin complexes for structure determination is generally difficult, computational docking can be a useful approach for understanding specific interactions. Previous studies used programs originally developed for docking small molecules to well-defined pockets, rather than for docking polysaccharides to highly charged shallow crevices that usually bind heparin. We have extended the program PIPER and the automated protein-protein docking server ClusPro to heparin docking. Using a molecular mechanics energy function for scoring and the fast Fourier transform correlation approach, the method generates and evaluates close to a billion poses of a heparin

SUBMITTER: Mottarella SE 

PROVIDER: S-EPMC4184157 | biostudies-literature | 2014 Jul

REPOSITORIES: biostudies-literature