PepPro: A Nonredundant Structure Data Set for Benchmarking Peptide-Protein Computational Docking.
J Comput Chem
; 41(4): 362-369, 2020 02 05.
Article
em En
| MEDLINE
| ID: mdl-31793016
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 ß-sheet, ß-sheet formed through binding, ß-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.
Palavras-chave
Texto completo:
1
Base de dados:
MEDLINE
Assunto principal:
Peptídeos
/
Proteínas
/
Conjuntos de Dados como Assunto
/
Química Computacional
Idioma:
En
Ano de publicação:
2020
Tipo de documento:
Article