We present here a novel approach for the efficient docking of peptides with known binding sequence motifs to their free receptor structures. We make use of our observation that a motif-based search can retrieve from the Protein Data Bank (PDB) structural fragments that are very similar to the peptide’s final, bound conformation. Fast and exhaustive global rigid body docking of these fragments using FFT based sampling predominantly identifies among top-ranking solutions a near-native conformation, with acceptable accuracy according to CAPRI peptide docking criteria.

Efficient global peptide docking using motif-derived fragments

251st National Meeting (2016)

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