1Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA2Department of Microbiology, Hebrew University, Jerusalem 91120, Israel3Department of Applied Mathematics and Statistics4Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
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SummaryWe 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 ImplementationThe method is available as part of the protein-protein docking server ClusPro at https://peptidock.cluspro.org/nousername.php.Contactmidas@laufercenter.org or email@example.comSupplementary informationSupplementary data are available at Bioinformatics online.