title: Modeling of protein-peptide interactions using the CABS-dock web server for binding site search and flexible docking.
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/.
authors.affiliation: Department of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
authors.forename: Maciej
authors.initials: M
authors.lastname: Blaszczyk
authors.affiliation: Department of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
authors.forename: Mateusz
authors.initials: M
authors.lastname: Kurcinski
authors.affiliation: Department of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
authors.forename: Maksim
authors.initials: M
authors.lastname: Kouza
authors.affiliation: Department of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
authors.forename: Lukasz
authors.initials: L
authors.lastname: Wieteska
authors.affiliation: Department of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
authors.forename: Aleksander
authors.initials: A
authors.lastname: Debinski
authors.affiliation: Department of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
authors.forename: Andrzej
authors.initials: A
authors.lastname: Kolinski
authors.affiliation: Department of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland. Electronic address: sekmi@chem.uw.edu.pl.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Kmiecik
mesh_terms: D001665:Binding Sites / Q000502:physiology; D008958:Models, Molecular; D062105:Molecular Docking Simulation / Q000379:methods*; D010455:Peptides / Q000737:chemistry / Q000378:metabolism*; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry / Q000378:metabolism*; D064878:Web Browser
chemical_list: D010455:Peptides; D011506:Proteins
keywords: CABS-dock; Flexible docking; Molecular docking; Peptide binding; Peptide folding; Protein–peptide docking