Jul 15, 2015

Modeling of protein-peptide interactions using the CABS-dock web server for binding site search and flexible docking

Methods : a Companion to Methods in Enzymology
Maciej BlaszczykSebastian Kmiecik

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 availabl...Continue Reading

Mentioned in this Paper

Molecular Dynamics
Gene Products, Protein
Tertiary Protein Structure
Appendix
Theoretical Study
Docking -molecular Interaction
Site
Ligand Binding Domain
Binding (Molecular Function)
Protein Domain

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