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PepPro: A Nonredundant Structure Data Set for Benchmarking Peptide–Protein Computational Docking
Author(s) -
Xu Xianjin,
Zou Xiaoqin
Publication year - 2020
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.26114
Subject(s) - docking (animal) , searching the conformational space for docking , peptide , benchmark (surveying) , beta sheet , macromolecular docking , benchmarking , protein structure , protein–ligand docking , protein structure prediction , computer science , algorithm , chemistry , molecular dynamics , biochemistry , computational chemistry , virtual screening , medicine , nursing , geodesy , marketing , business , geography
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 http://zoulab.dalton.missouri.edu/PepPro_benchmark. © 2019 Wiley Periodicals, Inc.