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XPairIt Docking Protocol for peptide docking and analysis

The mechanics of peptide–protein docking has long been an area of intense interest to the computational community. Here we discuss an improved docking protocol named XPairIt which uses a multitier approach, combining the PyRosetta docking software with the NAMD molecular dynamics package through a biomolecular simulation programming interface written in Python. This protocol is designed for systems where no a priori information of ligand structure (beyond sequence) or binding location is known. It provides for efficient incorporation of both ligand and target flexibility, is HPC-ready and is easily extensible for use of custom code. We apply this protocol to a set of 11 test cases drawn from benchmarking databases and from previously published studies for direct comparison with existing protocols. Strengths, weaknesses and areas of improvement are discussed.