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Identifying Protein-protein Interaction Sites Using Peptide Arrays

Identifying Protein-protein Interaction Sites Using Peptide Arrays

Published on: November 18, 2014

Comparison of two docking methods for peptide-protein interactions

Qiuying Yu^1,2, Fangyu Wang², Xiaofei Hu²

¹Avian Diseases Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.

Journal of the Science of Food and Agriculture

|January 10, 2018

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 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.

Keywords:

CScore KD value estimated accuracy peptide-protein docking

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