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

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. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.