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:
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).
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
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.