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Yu Q, Wang F, Hu X, Xing G, Deng R, Guo J, Cheng A, Wang J, Hao J, Zhao D, Teng M, Zhang G. Comparison of two docking methods for peptide-protein interactions. J Sci Food Agric 2018; 98:3722-3727. [PMID: 29315602 DOI: 10.1002/jsfa.8880] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 08/15/2017] [Accepted: 12/30/2017] [Indexed: 06/07/2023]
Abstract
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 KD values. The final results showed that a moderate correlation coefficient was represented between KD 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.
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Affiliation(s)
- Qiuying Yu
- Avian Diseases Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Henan Key Laboratory for Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Fangyu Wang
- Henan Key Laboratory for Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Xiaofei Hu
- Henan Key Laboratory for Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Guangxu Xing
- Henan Key Laboratory for Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Ruiguang Deng
- Henan Key Laboratory for Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Junqing Guo
- Henan Key Laboratory for Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Anchun Cheng
- Avian Diseases Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Jing Wang
- Henan Key Laboratory for Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Junfang Hao
- Henan Key Laboratory for Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Dong Zhao
- Henan Key Laboratory for Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Man Teng
- Henan Key Laboratory for Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Gaiping Zhang
- Avian Diseases Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Henan Key Laboratory for Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, China
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, People's Republic of China
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