CABS-dock
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:
11. Protocols for all-atom reconstruction and high-resolution refinement of protein-peptide complex structures
Methods in Molecular Biology, submitted, 201910. CABS-dock standalone: a toolbox for flexible protein-peptide docking
Bioinformatics, btz185, 20198. Highly Flexible Protein-Peptide Docking Using CABS-Dock
Methods in Molecular Biology, 1561: 69-94, 20177. A protocol for CABS-dock protein-peptide docking driven by side-chain contact information
Biomedical Engineering Online, 16, 20176. Modeling EphB4-EphrinB2 protein-protein interaction using flexible docking of a short linear motif
Biomedical Engineering Online, 16, 20175. Towards protein-protein docking with significant structural changes using CABS-dock
Proceedings Of The International Work-conference On Bioinformatics And Biomedical Engineering (iwwbio) In Granada, Spain, 207-213, Arxiv:1605.09266, 20164. Flexible protein-peptide docking using CABS-dock with knowledge about the binding site
Proceedings Of The International Work-conference On Bioinformatics And Biomedical Engineering (iwwbio) In Granada, Spain, 195-201, Arxiv:1605.09269, 20163. Modeling of protein-peptide interactions using the CABS-dock web server for binding site search and flexible docking
Methods, 93: 72-83, 20162. Protein-peptide molecular docking with large-scale conformational changes: the p53-MDM2 interaction
Scientific Reports, 6, 20161. CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site
Nucleic Acids Research, 43: W419-W424, 2015The 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
