Docking of peptides to GPCRs using a combination of CABS-dock with FlexPepDock refinement.

Briefings in Bioinformatics
Aleksandra Badaczewska-DawidMichał Koliński

Abstract

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.

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Citations

Jun 3, 2021·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Mateusz ZalewskiMichał Koliński
Jul 25, 2021·International Journal of Molecular Sciences·Mateusz KurcinskiAndrzej Kolinski

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Software Mentioned

flexPepDockingMinimizeOnly
PD2
ca2main
Modeller
GalaxyPepDock
ZDOCK
dock
- dock
nstruct
STAGE

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