Docking of peptides to GPCRs using a combination of CABS-dock with FlexPepDock refinement.
The structural description of peptide ligands bound to G protein-coupled receptors (GPCRs) is important for the discovery of new drugs and deeper understanding of the molecular mechanisms of life. Here we describe a three-stage protocol for the molecular docking of peptides to GPCRs using a set of different programs: (1) CABS-dock for docking fully flexible peptides; (2) PD2 method for the reconstruction of atomistic structures from C-alpha traces provided by CABS-dock and (3) Rosetta FlexPepDock for the refinement of protein-peptide complex structures and model scoring. We evaluated the proposed protocol on the set of seven different GPCR-peptide complexes (including one containing a cyclic peptide), for which crystallographic structures are available. We show that CABS-dock produces high resolution models in the sets of top-scored models. These sets of models, after reconstruction to all-atom representation, can be further improved by Rosetta high-resolution refinement and/or minimization, leading in most of the cases to sub-Angstrom accuracy in terms of interface root-mean-square-deviation measure.
['Badaczewska-Dawid|Aleksandra E|AE|', 'Kmiecik|Sebastian|S|', 'Koliński|Michał|M|0000-0003-1047-2186']
D030562:Databases, Protein D008024:Ligands D062105:Molecular Docking Simulation D010455:Peptides D043562:Receptors, G-Protein-Coupled
GPCR–peptide interaction flexible docking model refinement peptide docking peptide drugs receptor–peptide complex