UNRES-Dock - protein-protein and peptide-protein docking by coarse-grained replica-exchange MD simulations.

MOTIVATION The majority of the proteins in living organisms occur as homo- or hetero-multimeric structures. While there are many tools to predict the structures of single-chain proteins or protein complexes with small ligands, peptide-protein and protein-protein docking is more challenging. In this work, we utilized multiplexed replica exchange MD simulations with the physics-based heavily coarse-grained UNRES model, which provides more than a 1000-fold simulation speed-up compared to all-atom approaches to predict structures of protein complexes. RESULTS We present a new protein-protein and peptide-protein docking functionality of the UNRES package, which includes a variable degree of conformational flexibility. UNRES-Dock protocol was tested on a set of 55 complexes with size from 43 to 587 amino-acid residues, showing that structures of the complexes can be predicted with good quality, if the sampling of the conformational space is sufficient, especially for flexible peptide-protein systems. The developed automatized protocol has been implemented in the standalone UNRES package and in the UNRES server. AVAILABILITY UNRES server: http://unres-server.chem.ug.edu.pl; UNRES package: http://unres.pl. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.