ClusPro PeptiDock: Efficient global docking of peptide recognition motifs using FFT

Kathryn A. Porter, Bing Xia, Dmitri Beglov, Tanggis Bohnuud, Nawsad Alam, Ora Schueler-Furman, Dima Kozakov*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

80 Scopus citations

Abstract

Summary We present an approach for the efficient docking of peptide motifs to their free receptor structures. Using a motif based search, we can retrieve structural fragments from the Protein Data Bank (PDB) that are very similar to the peptide's final, bound conformation. We use a Fast Fourier Transform (FFT) based docking method to quickly perform global rigid body docking of these fragments to the receptor. According to CAPRI peptide docking criteria, an acceptable conformation can often be found among the top-ranking predictions. Availability and Implementation The method is available as part of the protein-protein docking server ClusPro at https://peptidock.cluspro.org/nousername.php. Contact midas@laufercenter.org or oraf@ekmd.huji.ac.il Supplementary informationSupplementary dataare available at Bioinformatics online.

Original languageAmerican English
Pages (from-to)3299-3301
Number of pages3
JournalBioinformatics
Volume33
Issue number20
DOIs
StatePublished - 15 Oct 2017

Bibliographical note

Publisher Copyright:
© The Author 2017. Published by Oxford University Press. All rights reserved.

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