Rosetta FlexPepDock web server - High resolution modeling of peptide-protein interactions

Nir London, Barak Raveh, Eyal Cohen, Guy Fathi, Ora Schueler-Furman*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

303 Scopus citations


Peptide-protein interactions are among the most prevalent and important interactions in the cell, but a large fraction of those interactions lack detailed structural characterization. The Rosetta FlexPepDock web server ( provides an interface to a high-resolution peptide docking (refinement) protocol for the modeling of peptide-protein complexes, implemented within the Rosetta framework. Given a protein receptor structure and an approximate, possibly inaccurate model of the peptide within the receptor binding site, the FlexPepDock server refines the peptide to high resolution, allowing full flexibility to the peptide backbone and to all side chains. This protocol was extensively tested and benchmarked on a wide array of non-redundant peptide-protein complexes, and was proven effective when applied to peptide starting conformations within 5.5 backbone root mean square deviation from the native conformation. FlexPepDock has been applied to several systems that are mediated and regulated by peptide-protein interactions. This easy to use and general web server interface allows non-expert users to accurately model their specific peptide-protein interaction of interest.

Original languageAmerican English
Pages (from-to)W249-W253
JournalNucleic Acids Research
Issue numberSUPPL. 2
StatePublished - 1 Jul 2011

Bibliographical note

Funding Information:
Israel Science Foundation, founded by the Israel Academy of Science and Humanities (grant number 306/6); USA– Israel Binational Science Foundation (grant number 2009418); National Institutes of Health (GM40602). Converging Technologies Scholarship funded by the Planning and Budgeting Committee of the Israeli Council for higher education (to N.L.). Funding for open access charge: USA–Israel Binational Science Foundation (grant number 2009418).


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