Homology Modeling pp 375-398

Part of the Methods in Molecular Biology book series (MIMB, volume 857) | Cite as

Modeling Peptide–Protein Interactions

Protocol

Abstract

Peptide–protein interactions are prevalent in the living cell and form a key component of the overall protein–protein interaction network. These interactions are drawing increasing interest due to their part in signaling and regulation, and are thus attractive targets for computational structural modeling. Here we report an overview of current techniques for the high resolution modeling of peptide–protein complexes. We dissect this complicated challenge into several smaller subproblems, namely: modeling the receptor protein, predicting the peptide binding site, sampling an initial peptide backbone conformation and the final refinement of the peptide within the receptor binding site. For each of these conceptual stages, we present available tools, approaches, and their reported performance. We summarize with an illustrative example of this process, highlighting the success and current challenges still facing the automated blind modeling of peptide–protein interactions. We believe that the upcoming years will see considerable progress in our ability to create accurate models of peptide–protein interactions, with applications in binding-specificity prediction, rational design of peptide-mediated interactions and the usage of peptides as therapeutic agents.

Key words

Peptide docking Peptide modeling Rosetta FlexPepDock Peptide–protein interactions Peptide–protein complexes Peptide binding 

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Copyright information

© Springer Science+Business Media,LLC 2011

Authors and Affiliations

  1. 1.Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Hadassah Medical SchoolThe Hebrew UniversityJerusalemIsrael
  2. 2.The Blavatnik School of Computer ScienceTel-Aviv UniversityRamat AvivIsrael

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