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Protein-peptide interactions play a key role in cell functions. Theirstructural characterization, though challenging, is important for the discoveryof new drugs. The CABS-dock web server provides an interface for modelingprotein-peptide interactions using a highly efficient protocol for the flexibledocking of peptides to proteins. While other docking algorithms requirepre-defined localization of the binding site, CABS-dock doesn't require suchknowledge. Given a protein receptor structure and a peptide sequence (andstarting from random conformations and positions of the peptide), CABS-dockperforms simulation search for the binding site allowing for full flexibilityof the peptide and small fluctuations of the receptor backbone. This protocolwas extensively tested over the largest dataset of non-redundantprotein-peptide interactions available to date (including bound and unbounddocking cases). For over 80% of bound and unbound data set cases, we obtainedmodels with high or medium accuracy (sufficient for practical applications).Additionally, as optional features, CABS-dock can exclude user-selected bindingmodes from docking search or to increase the level of flexibility for chosenreceptor fragments. CABS-dock is freely available as a web server athttp://biocomp.chem.uw.edu.pl/CABSdock

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