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:

12. Flexible docking of peptides to proteins using CABS-dock

Protein Science, 29: 211–222, 2020
Kurciński Mateusz , Badaczewska-Dawid Aleksandra, Kolinski Michal, Kolinski Andrzej, Kmiecik Sebastian

11. Protocols for all-atom reconstruction and high-resolution refinement of protein-peptide complex structures

Methods in Molecular Biology, submitted, 2019
Badaczewska-Dawid Aleksandra, Khramushin Alisa, Kolinski Andrzej, Schueler-Furman Ora, Kmiecik Sebastian

10. CABS-dock standalone: a toolbox for flexible protein-peptide docking

Bioinformatics, btz185, 2019
Kurciński Mateusz , Ciemny M. P., Oleniecki T., Kuriata Aleksander, Badaczewska-Dawid A. E., Kolinski A., Kmiecik Sebastian

8. Highly Flexible Protein-Peptide Docking Using CABS-Dock

Methods in Molecular Biology, 1561: 69-94, 2017
Ciemny Maciej, Kurciński Mateusz , Konrad Kozak, Andrzej Kolinski, Kmiecik Sebastian

5. 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, 2016
Ciemny Maciej, Kurciński Mateusz , Andrzej Koliński, Kmiecik Sebastian

4. 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, 2016
Kurciński Mateusz , Ciemny Maciej, Błaszczyk Maciej, Andrzej Koliński, Kmiecik Sebastian

The movies below show some examples of CABS-dock simulations: