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.
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 webserver 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:
1. 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, 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 input information).
2. Modeling of protein-peptide interactions using the CABS-dock web server for binding site search and flexible docking
Methods, 93: 72-83, 2016 - the paper presents: example CABS-dock results obtained in the default mode and using advanced options that enable to increase the range of flexibility for chosen receptor fragments, examples of scoring of CABS-dock models using all-atom molecular dynamics, a tutorial appendix for analysis and visualization of CABS-dock results using VMD
3. CABS-dock standalone: a toolbox for flexible protein-peptide docking
Bioinformatics, btz185, 2019 - the paper presents CABS-dock standalone package. In comparison to the webserver version, the standalone package offers much more functionalities that support docking with different kinds of knowledge about the modeled protein-peptide system.
4. Protein-peptide molecular docking with large-scale conformational changes: the p53-MDM2 interaction
Scientific Reports, 6, 2016 - the paper presents CABS-dock application to simulations of the binding of the p53-MDM2 complex, including large-scale structural rearrangements of MDM2 flexible regions5. Highly Flexible Protein-Peptide Docking Using CABS-Dock
Methods 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 scripts6. Protein-peptide docking using CABS-dock and contact information
Briefings 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.7. Modeling EphB4-EphrinB2 protein-protein interaction using flexible docking of a short linear motif
Biomedical Engineering Online, 16, 2017 - the paper presents an example test case of the protocol for protein-protein docking in which CABS-dock is used for docking a short linear motif as a peptide. Furthermore, based on the docking result, the protein–protein complex is reconstructed and refined8. A protocol for CABS-dock protein-peptide docking driven by side-chain contact information
Biomedical Engineering Online, 16, 2017 - the paper shows preeliminary studies that were further continued in the work number 5.9. Towards protein-protein docking with significant structural changes using CABS-dock
Proceedings Of The International Work-conference On Bioinformatics And Biomedical Engineering In Granada, Spain, 207-213, Arxiv:1605.09266, 2016 - the paper presents preeliminary studies that were further continued in the work number 6.10. Flexible protein-peptide docking using CABS-dock with knowledge about the binding site
Proceedings Of The International Work-conference On Bioinformatics And Biomedical Engineering In Granada, Spain, 195-201, Arxiv:1605.09269, 2016- 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
