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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\u2013peptide complex structures and model scoring. We evaluated the proposed protocol on the set of seven different GPCR\u2013peptide 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.<\/jats:p>","DOI":"10.1093\/bib\/bbaa109","type":"journal-article","created":{"date-parts":[[2020,5,8]],"date-time":"2020-05-08T07:09:38Z","timestamp":1588921778000},"source":"Crossref","is-referenced-by-count":16,"title":["Docking of peptides to GPCRs using a combination of CABS-dock with FlexPepDock refinement"],"prefix":"10.1093","volume":"22","author":[{"given":"Aleksandra 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