title: Highly Flexible Protein-Peptide Docking Using CABS-Dock.
abstract: Protein-peptide molecular docking is a difficult modeling problem. It is even more challenging when significant conformational changes that may occur during the binding process need to be predicted. In this chapter, we demonstrate the capabilities and features of the CABS-dock server for flexible protein-peptide docking. CABS-dock allows highly efficient modeling of full peptide flexibility and significant flexibility of a protein receptor. During CABS-dock docking, the peptide folding and binding process is explicitly simulated and no information about the peptide binding site or its structure is used. This chapter presents a successful CABS-dock use for docking a potentially therapeutic peptide to a protein target. Moreover, simulation contact maps, a new CABS-dock feature, are described and applied to the docking test case. Finally, a tutorial for running CABS-dock from the command line or command line scripts is provided. The CABS-dock web server is available from http://biocomp.chem.uw.edu.pl/CABSdock/ .
authors.affiliation: Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland.
authors.forename: Maciej Paweł
authors.initials: MP
authors.lastname: Ciemny
authors.affiliation: Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland.
authors.forename: Mateusz
authors.initials: M
authors.lastname: Kurcinski
authors.affiliation: Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland.
authors.forename: Konrad Jakub
authors.initials: KJ
authors.lastname: Kozak
authors.affiliation: Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland.
authors.forename: Andrzej
authors.initials: A
authors.lastname: Kolinski
authors.affiliation: Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland. sekmi@chem.uw.edu.pl.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Kmiecik
mesh_terms: D001665:Binding Sites; D030562:Databases, Protein; D006801:Humans; D008958:Models, Molecular; D062105:Molecular Docking Simulation; D010446:Peptide Fragments / Q000737:chemistry* / Q000378:metabolism*; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry / Q000378:metabolism*; D012984:Software; D064878:Web Browser
chemical_list: D010446:Peptide Fragments; D011506:Proteins
keywords: CABS; Computational modeling; Molecular docking; Peptide binding; Peptide design; Protein-peptide interactions