Sub-angstrom modeling of complexes between flexible peptides and globular proteins

Barak Raveh, Nir London, Ora Schueler-Furman*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

331 Scopus citations


A wide range of regulatory processes in the cell are mediated by flexible peptides that fold upon binding to globular proteins. Computational efforts to model these interactions are hindered by the large number of rotatable bonds in flexible peptides relative to typical ligand molecules, and the fact that different peptides assume different backbone conformations within the same binding site. In this study, we present Rosetta FlexPepDock, a novel tool for refining coarse peptide-protein models that allows significant changes in both peptide backbone and side chains. We obtain high resolution models, often of sub-angstrom backbone quality, over an extensive and general benchmark that is based on a large nonredundant dataset of 89 peptide-protein interactions. Importantly, side chains of known binding motifs are modeled particularly well, typically with atomic accuracy. In addition, our protocol has improved modeling quality for the important application of cross docking to PDZ domains. We anticipate that the ability to create high resolution models for a wide range of peptide-protein complexes will have significant impact on structure-based functional characterization, controlled manipulation of peptide interactions, and on peptide-based drug design.

Original languageAmerican English
Pages (from-to)2029-2040
Number of pages12
JournalProteins: Structure, Function and Bioinformatics
Issue number9
StatePublished - Jul 2010


  • Linear binding motifs
  • Peptide docking
  • Peptide-mediated interactions
  • Peptide-protein interactions
  • Rosetta flexpepdock
  • Short peptides


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