MDockPeP: An ab‐initio protein–peptide docking server

Protein–peptide interactions play a crucial role in a variety of cellular processes. The protein–peptide complex structure is a key to understand the mechanisms underlying protein–peptide interactions and is critical for peptide therapeutic development. We present a user‐friendly protein–peptide docking server, MDockPeP. Starting from a peptide sequence and a protein receptor structure, the MDockPeP Server globally docks the all‐atom, flexible peptide to the protein receptor. The produced modes are then evaluated with a statistical potential‐based scoring function, ITScorePeP. This method was systematically validated using the peptiDB benchmarking database. At least one near‐native peptide binding mode was ranked among top 10 (or top 500) in 59% (85%) of the bound cases, and in 40.6% (71.9%) of the challenging unbound cases. The server can be used for both protein–peptide complex structure prediction and initial‐stage sampling of the protein–peptide binding modes for other docking or simulation methods. MDockPeP Server is freely available at http://zougrouptoolkit.missouri.edu/mdockpep . © 2018 Wiley Periodicals, Inc.