Format

Send to

Choose Destination
Methods. 2016 Jan 15;93:72-83. doi: 10.1016/j.ymeth.2015.07.004. Epub 2015 Jul 10.

Modeling of protein-peptide interactions using the CABS-dock web server for binding site search and flexible docking.

Author information

1
Department of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
2
Department of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland. Electronic address: sekmi@chem.uw.edu.pl.

Abstract

Protein-peptide interactions play essential functional roles in living organisms and their structural characterization is a hot subject of current experimental and theoretical research. Computational modeling of the structure of protein-peptide interactions is usually divided into two stages: prediction of the binding site at a protein receptor surface, and then docking (and modeling) the peptide structure into the known binding site. This paper presents a comprehensive CABS-dock method for the simultaneous search of binding sites and flexible protein-peptide docking, available as a user's friendly web server. We present example CABS-dock results obtained in the default CABS-dock mode and using its advanced options that enable the user to increase the range of flexibility for chosen receptor fragments or to exclude user-selected binding modes from docking search. Furthermore, we demonstrate a strategy to improve CABS-dock performance by assessing the quality of models with classical molecular dynamics. Finally, we discuss the promising extensions and applications of the CABS-dock method and provide a tutorial appendix for the convenient analysis and visualization of CABS-dock results. The CABS-dock web server is freely available at http://biocomp.chem.uw.edu.pl/CABSdock/.

KEYWORDS:

CABS-dock; Flexible docking; Molecular docking; Peptide binding; Peptide folding; Protein–peptide docking

PMID:
26165956
DOI:
10.1016/j.ymeth.2015.07.004
[Indexed for MEDLINE]
Free full text

Supplemental Content

Full text links

Icon for Elsevier Science
Loading ...
Support Center