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.
CABS-dock is a global docking tool for protein-peptide docking (see our review on protein-peptide docking). CABS-dock implements the CABS coarse-grained protein model for fast modeling of protein and peptide flexibility during search for the binding site. CABS-dock is available as easy-to-use web server and as the standalone package. In comparison to the web server version, the 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:
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