Today we officially launched the CABS-dock web server for protein-peptide docking. CABS-dock allows for docking without prior knowledge of the peptide binding site.
Given a protein receptor structure and a peptide sequence, CABS-dock performs docking search for the binding site allowing for full flexibility of the peptide and small fluctuations of the receptor backbone.
The CABS-dock is freely available at http://biocomp.chem.uw.edu.pl/CABSdock/
Below, the docking trajectory generated by CABS-dock for the major histocompatibility complex (MHC)-peptide structure (PDB accession code 3BWA) is presented. Experimental peptide structure is shown in green, while the simulated peptide in red. The movie shows 1 of 10 trajectories generated in a standard CABS-dock simulation run. During simulation, no information about the binding site was used (CABS-dock simulations start from random conformations and positions of the peptide). The root mean square deviation of the peptide at the simulation end is within 1.83 Angstroms from the experimental structure.
The CABS-dock methodology has been also recently used to modeling of folding and binding of an intrinsically disordered peptide. Below is the the movie from the study of Kurcinski M, Kolinski A and Kmiecik S. "Mechanism of Folding and Binding of an Intrinsically Disordered Protein as Revealed by Ab Initio Simulations". Journal of Chemical Theory and Computation, doi: 10.1021/ct500287c, 2014