A protocol for CABS-dock protein-peptide docking driven by side-chain contact information.

ABSTRACT:

Background

The characterization of protein-peptide interactions is a challenge for computational molecular docking. Protein-peptide docking tools face at least two major difficulties: (1) efficient sampling of large-scale conformational changes induced by binding and (2) selection of the best models from a large set of predicted structures. In this paper, we merge an efficient sampling technique with external information about side-chain contacts to sample and select the best possible models.

Methods

In this paper we test a new protocol that uses information about side-chain contacts in CABS-dock protein-peptide docking. As shown in our recent studies, CABS-dock enables efficient modeling of large-scale conformational changes without knowledge about the binding site. However

SUBMITTER: Kurcinski M 

PROVIDER: S-EPMC5568604 | biostudies-literature | 2017 Aug

REPOSITORIES: biostudies-literature