PepPro: A Nonredundant Structure Data Set for Benchmarking Peptide-Protein Computational Docking.

ABSTRACT: 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.

SUBMITTER: Xu X 

PROVIDER: S-EPMC7447090 | biostudies-literature | 2020 Feb

REPOSITORIES: biostudies-literature