Highly flexible protein-peptide docking using CABS-dock

TL;DR

CABS-dock is a flexible protein-peptide docking tool that explicitly simulates peptide folding and receptor flexibility without prior binding site information, demonstrated through therapeutic peptide docking.

Contribution

This work introduces CABS-dock, a novel server enabling highly flexible, ab initio protein-peptide docking with explicit simulation of peptide and receptor conformational changes.

Findings

Successfully docked therapeutic peptide to target protein

Introduced simulation contact maps as a new feature

Provided a user-friendly web server and tutorial

Abstract

Protein-peptide molecular docking is a difficult modeling problem. It is even more challenging when significant conformational changes that may occur during the binding process need to be predicted. In this chapter, we demonstrate the capabilities and features of the CABS-dock server for flexible protein-peptide docking. CABS-dock allows highly efficient modeling of full peptide flexibility and significant flexibility of a protein receptor. During CABS-dock docking, the peptide folding and binding process is explicitly simulated and no information about the peptide binding site or its structure, is used. This chapter presents a successful CABS-dock use for docking a potentially therapeutic peptide to a protein target. Moreover, simulation contact maps, a new CABS-dock feature, are described and applied to the docking test case. Finally, a tutorial for running CABS-dock from the command line or command line scripts is provided. The CABS-dock web server is available from http://biocomp.chem.uw.edu.pl/CABSdock/