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. 2017 Oct 15;33(20):3299-3301.
doi: 10.1093/bioinformatics/btx216.

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

Kathryn A Porter  1 , Bing Xia  1 , Dmitri Beglov  1 , Tanggis Bohnuud  1 , Nawsad Alam  2 , Ora Schueler-Furman  2 , Dima Kozakov  3   4
Affiliations

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

Kathryn A Porter et al. Bioinformatics. .

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 information: Supplementary data are available at Bioinformatics online.

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Figures

Fig. 1
Fig. 1
Examples for models generated by PeptiDock rigid body docking of peptides to a receptor. Receptor structures are shown in light grey. Silver structures represent the native peptide pose. (A) A peptide derived from CDC6 with the sequence motif KGRRL is successfully docked to cyclin. The third ranked prediction (dark grey) produces an acceptable accuracy result (1.9Å backbone RMSD; apo/holo PDB IDs: 1H1R/2CCH). (B) No near native structure is sampled using the standard energy function weight set when a peptide derived from synaptojanin is docked to the ap2 adaptor (apo/holo PDB IDs: 1B9K/2VJ0). Nevertheless, a 4.0Å RMSD model (gray) is produced when an electrostatics-favored coefficient set is used in place of the standard weight set. This can be explained by the fact that this interaction is dominated by several hydrogen bonds of the peptide backbone (dotted line) in the native complex, but lacks strong hydrophobic interactions with the aromatic side chains, as well as by crystal contacts in the bound conformation (shown in opaque gray sticks) that stabilize the solved peptide conformation. The hydrophobic V6 points into the “solvent”, but actually contacts the symmetry mate (interaction is marked with *; see Figure S3 for more details) (Color version of this figure is available at Bioinformatics online.)
See this image and copyright information in PMC

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