Highly Flexible Protein-Peptide Docking Using CABS-Dock

  • Maciej Paweł Ciemny
  • Mateusz Kurcinski
  • Konrad Jakub Kozak
  • Andrzej Kolinski
  • Sebastian Kmiecik
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1561)

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/.

Key words

Protein-peptide interactions Molecular docking CABS Peptide binding Peptide design Computational modeling 

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Copyright information

© Springer Science+Business Media LLC 2017

Authors and Affiliations

  • Maciej Paweł Ciemny
    • 1
  • Mateusz Kurcinski
    • 1
  • Konrad Jakub Kozak
    • 1
  • Andrzej Kolinski
    • 1
  • Sebastian Kmiecik
    • 1
  1. 1.Faculty of ChemistryUniversity of WarsawWarsawPoland

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