CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site

By Mateusz Kurcinski, Michal Jamróz, Maciej Blaszczyk, Andrzej Kolinski, Sebastian Kmiecik. 2015

295 citations recorded by the source corpus.

Protein–peptide interactions play a key role in cell functions. Their structural characterization, though challenging, is important for the discovery of new drugs. The CABS-dock web server provides an interface for modeling protein–peptide interactions using a highly efficient protocol for the flexible docking of peptides to proteins. While other docking algorithms require pre-defined localization of the binding site, CABS-dock does not require such knowledge. Given a protein receptor structure and a peptide sequence (and starting from random conformations and positions of the peptide), CABS-dock performs simulation search for the binding site allowing for full flexibility of the peptide and small fluctuations of the receptor backbone. This protocol was extensively tested over the largest dataset of non-redundant protein–peptide interactions available to date (including bound and unbound docking cases). For over 80% of bound and unbound dataset cases, we obtained models with high or medium accuracy (sufficient for practical applications). Additionally, as optional features, CABS-dock can exclude user-selected binding modes from docking search or to increase the level of flexibility for chosen receptor fragments. CABS-dock is freely available as a web server at http://biocomp.chem.uw.edu.pl/CABSdock.

Subfields: Computational Theory and Mathematics, Molecular Biology, Radiology, Nuclear Medicine and Imaging

Citations in the corpus

• HPEPDOCK: a web server for blind peptide–protein docking based on a hierarchical algorithm (2018, unknown): “Recently, several global peptide docking algorithms such as AnchorDock (12), CABS-dock (10), pepATTRACT (8) and MDockPep (7) have been developed for the blind prediction of protein–peptide complexes, among which CABS-dock is available as a web server and pepATRRACT has a web version for its rigid…”
• High-resolution global peptide-protein docking using fragments-based PIPER-FlexPepDock (2017, unknown): “The CABS-dock protocol uses randomly generated peptide conformations based on either predicted or known secondary structure, randomly orients these peptides over the receptor surface, and refines them using replica exchange Monte Carlo dynamics [15].”
• PEP-FOLD3: faster de novo structure prediction for linear peptides in solution and in complex (2016, unknown): “The RosettaFlexPepDock (19) server will refine the structure of a peptide bound to a receptor, Galaxypepdock (20) performs similarity based docking using existing templates and the CABS-dock server (21) performs a blind docking which can be time consuming.”
• Improving peptide-protein docking with AlphaFold-Multimer using forced sampling (2021, unknown): “CABS-dock utilizes a simulation search with flexible peptide and receptor for peptide-protein docking (Kurcinski et al., 2015; Ciemny et al., 2017).”