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.
Protein-peptide docking methods can be divided into three categories: template-based docking; local docking; and global docking (see our review paper on protein-peptide docking and its video summary below).
CABS-dock is a global docking tool that implements the CABS simulation engine (which is the coarse-grained protein model reviewed here) for fast modeling of protein and peptide flexibility during search for the binding site. CABS-dock is presently available as the web server and as the standalone package. In comparison to web server version, standalone package offers much more functionalities that support docking with different kinds of knowledge about the modeled protein-peptide system.
The functionalities and applications of the CABS-dock method have been described so far in the following papers:
Nucleic Acids Research, 43: W419-W424, 2015 - the paper describes CABS-dock web server implementation and results
obtained for the PeptiDB benchmark set in the default mode (using
peptide sequence, peptide secondary structure and receptor structure
4. Highly Flexible Protein-Peptide Docking Using CABS-DockMethods in Molecular Biology, 1561: 69-94, 2017 - the paper presents an example of CABS-dock application for docking a
potentially therapeutic peptide to a protein target, simulation contact
maps (a new feature of the web server), tutorial for running CABS-dock
web server from the command line or command line scripts
5. Protein-peptide docking using CABS-dock and contact informationBriefings in Bioinformatics, bby080, 2018 - the paper presents a specific CABS-dock protocol that enhances the
docking procedure using fragmentary information about protein–peptide
contacts. The contact information is used to narrow down the search for
the binding peptide pose to the proximity of the binding site.
The movies below show some examples of CABS-dock simulations:
- simulation of binding of MDM2 protein receptor and p53 peptide with large-scale conformational changes of disordered MDM2 fragments that has been described here
- simulations of folding and binding of the disordered pKID peptide to KIX protein receptor that has been described here