Protein-peptide docking using CABS-dock and contact information.

Autor: Blaszczyk M; Biological and Chemical Research Centre, University of Warsaw., Ciemny MP; Faculty of Physics at the University of Warsaw., Kolinski A; University of Warsaw., Kurcinski M; Biological and Chemical Research Centre, University of Warsaw., Kmiecik S; Biological and Chemical Research Centre, University of Warsaw.
Jazyk: angličtina
Zdroj: Briefings in bioinformatics [Brief Bioinform] 2019 Nov 27; Vol. 20 (6), pp. 2299-2305.
DOI: 10.1093/bib/bby080
Abstrakt: CABS-dock is a computational method for protein-peptide molecular docking that does not require predefinition of the binding site. The peptide is treated as fully flexible, while the protein backbone undergoes small fluctuations and, optionally, large-scale rearrangements. Here, we present a specific CABS-dock protocol that enhances the docking procedure using fragmentary information about protein-peptide contacts. The contact information is used to narrow down the search for the binding peptide pose to the proximity of the binding site. We used information on a single-chosen and randomly chosen native protein-peptide contact to validate the protocol on the peptiDB benchmark. The contact information significantly improved CABS-dock performance. The protocol has been made available as a new feature of the CABS-dock web server (at http://biocomp.chem.uw.edu.pl/CABSdock/).
Short Abstract: CABS-dock is a tool for flexible docking of peptides to proteins. In this article, we present a protocol for CABS-dock docking driven by information about protein-peptide contact(s). Using information on individual protein-peptide contacts allows to improve the accuracy of CABS-dock docking.
(© The Author(s) 2018. Published by Oxford University Press.)
Databáze: MEDLINE
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