Modeling peptide-protein interactions

Nir London, Barak Raveh, Ora Schueler-Furman*

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review

23 Scopus citations


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.

Original languageAmerican English
Title of host publicationHomology Modeling
Subtitle of host publicationMethods and Protocols
EditorsAndrew Orry, Ruben Abagyan
Number of pages24
StatePublished - 2012

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745


  • Peptide binding
  • Peptide docking
  • Peptide modeling
  • Peptide-protein complexes
  • Peptide-protein interactions
  • Rosetta FlexPepDock


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