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Comparison of two docking methods for peptide‐protein interactions
Author(s) -
Yu Qiuying,
Wang Fangyu,
Hu Xiaofei,
Xing Guangxu,
Deng Ruiguang,
Guo Junqing,
Cheng Anchun,
Wang Jing,
Hao Junfang,
Zhao Dong,
Teng Man,
Zhang Gaiping
Publication year - 2018
Publication title -
journal of the science of food and agriculture
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.782
H-Index - 142
eISSN - 1097-0010
pISSN - 0022-5142
DOI - 10.1002/jsfa.8880
Subject(s) - docking (animal) , peptide , searching the conformational space for docking , computational biology , chemistry , protein–ligand docking , protein structure , biochemistry , biology , drug discovery , medicine , virtual screening , nursing
BACKGROUND The importance of peptides in regulatory interactions has caused peptide‐protein docking to attract the attention of many researchers. A variety of methods for molecular modeling of peptide‐protein docking, such as local search and global search, are currently used. RESULTS The interactions of 11 peptides and CSFV E2 protein were evaluated by the GalaxyPepDock and FlexX/ SYBYL programs, respectively. The assessment scores of all the peptides were correlated with their K D values. The final results showed that a moderate correlation coefficient was represented between K D values and CScores of predicted models by FlexX/ SYBYL. CONCLUSION Our results demonstrate that considering the flexibility of the peptide is better than searching for more potential binding sites on the target protein surface while performing peptide‐protein molecular docking. These data provide reasonable evidence for the molecular design of peptides and guidance for the functional assignment of target proteins. © 2018 Society of Chemical Industry