AutoDock CrankPep: combining folding and docking to predict protein-peptide complexes

Protein-peptide interactions mediate a wide variety of cellular and biological functions. Methods for predicting these interactions have garnered a lot of interest over the past few years, as witnessed by the rapidly growing number of peptide-based therapeutic molecules currently in clinical trials. The size and flexibility of peptides has shown to be challenging for existing automated docking software programs. Here we present AutoDock CrankPep or ADCP in short, a novel approach to dock flexible peptides into rigid receptors. ADCP folds a peptide in the potential field created by the protein to predict the protein-peptide complex. We show that it outperforms leading peptide docking methods on two protein-peptide datasets commonly used for benchmarking docking methods: LEADS-PEP and peptiDB, comprised of peptides with up to 15 amino acids in length. Beyond these datasets, ADCP reliably docked a set of protein-peptide complexes containing peptides ranging in lengths from 16 to 20 amino acids. The robust performance of ADCP on these longer peptides enables accurate modeling of peptide-mediated protein-protein interactions and interactions with disordered proteins. ADCP is distributed under the LGPL 2.0 open source license and is available at http://adcp.scripps.edu. The source code is available at https://github.com/ccsb-scripps/ADCP. Supplementary data are available at Bioinformatics online.