Fully Blind Peptide-Protein Docking with pepATTRACT

Christina E.M. Schindler, Sjoerd J. De Vries, Martin Zacharias

Research output: Contribution to journalArticlepeer-review

96 Scopus citations

Abstract

Summary Peptide-protein interactions are ubiquitous in the cell and form an important part of the interactome. Computational docking methods can complement experimental characterization of these complexes, but current protocols are not applicable on the proteome scale. Here, we present a new fully blind flexible peptide-protein docking protocol, pepATTRACT, which combines a rapid coarse-grained global peptide docking search of the entire protein surface with a two-stage atomistic flexible refinement. Global unbound-unbound docking yielded near-native models for 70% of the docking cases when testing the protocol on the largest benchmark of peptide-protein complexes available to date. This performance is similar to that of state-of-the-art local docking protocols that rely on information about the binding site. Upon restricting the search to the peptide binding region, the resulting pepATTRACT-local approach outperformed existing methods. Docking scripts for pepATTRACT and pepATTRACT-local can be generated via a web interface at www.attract.ph.tum.de/peptide.html.

Original languageEnglish
Article number3205
Pages (from-to)1507-1515
Number of pages9
JournalStructure
Volume23
Issue number8
DOIs
StatePublished - 7 Aug 2015
Externally publishedYes

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