Feb 27, 2017

Highly Flexible Protein-Peptide Docking Using CABS-Dock

Methods in Molecular Biology
Maciej Pawel CiemnySebastian Kmiecik

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/ .

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Mentioned in this Paper

Gene Products, Protein
Molecular Docking Simulation
Plasma Protein Binding Capacity
Docking -molecular Interaction
Computer Programs and Programming
Peptide Fragments
Protein Conformation
Binding (Molecular Function)
Molecular Docking Analysis
Structure

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