Rosetta FlexPepDock ab-initio: simultaneous folding, docking and refinement of peptides onto their receptors.

ABSTRACT: Flexible peptides that fold upon binding to another protein molecule mediate a large number of regulatory interactions in the living cell and may provide highly specific recognition modules. We present Rosetta FlexPepDock ab-initio, a protocol for simultaneous docking and de-novo folding of peptides, starting from an approximate specification of the peptide binding site. Using the Rosetta fragments library and a coarse-grained structural representation of the peptide and the receptor, FlexPepDock ab-initio samples efficiently and simultaneously the space of possible peptide backbone conformations and rigid-body orientations over the receptor surface of a given binding site. The subsequent all-atom refinement of the coarse-grained models includes full side-chain modeling of both the recepto

SUBMITTER: Raveh B 

PROVIDER: S-EPMC3084719 | biostudies-literature | 2011 Apr

REPOSITORIES: biostudies-literature