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Modeling Peptide-Protein Interactions

Volume 1561 of the series Methods in Molecular Biology pp 69-94

Date:

Highly Flexible Protein-Peptide Docking Using CABS-Dock

  • Maciej Paweł CiemnyAffiliated withFaculty of Chemistry, University of Warsaw 
  • , Mateusz KurcinskiAffiliated withFaculty of Chemistry, University of Warsaw 
  • , Konrad Jakub KozakAffiliated withFaculty of Chemistry, University of Warsaw
  • , Andrzej KolinskiAffiliated withFaculty of Chemistry, University of Warsaw
  • , Sebastian KmiecikAffiliated withFaculty of Chemistry, University of Warsaw Email author 

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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