We present a nonredundant benchmark, coined PepPro, for testing peptide–protein docking algorithms. Currently, PepPro contains 89 nonredundant experimentally determined peptide–protein complex structures, with peptide sequence lengths ranging from 5 to 30 amino acids. The benchmark covers peptides with distinct secondary structures, including helix, partial helix, a mixture of helix and β‐sheet, β‐sheet formed through binding, β‐sheet formed through self‐folding, and coil. In addition, unbound proteins' structures are provided for 58 complexes and can be used for testing the ability of a docking algorithm handling the conformational changes of proteins during the binding process. PepPro should benefit the docking community for the development and improvement of peptide docking algorithms. The benchmark is available at
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
- NSF-PAR ID:
- 10078233
- Publisher / Repository:
- Wiley Blackwell (John Wiley & Sons)
- Date Published:
- Journal Name:
- Journal of Computational Chemistry
- Volume:
- 39
- Issue:
- 28
- ISSN:
- 0192-8651
- Page Range / eLocation ID:
- p. 2409-2413
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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