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A Random Forest Model for Peptide Classification Based on Virtual Docking Data

文献类型： 外文期刊

作者： Feng, Hua 1 ; Wang, Fangyu 1 ; Li, Ning 1 ; Xu, Qian 1 ; Zheng, Guanming 2 ; Sun, Xuefeng 1 ; Hu, Man 1 ; Xing, Guangxu 1 ; Zhang, Gaiping 1 ;

作者机构： 1.Henan Acad Agr Sci, Key Lab Anim Immunol, Zhengzhou 450002, Peoples R China

2.Henan Univ Chinese Med, Publ Hlth & Prevent Med Teaching & Res Ctr, Zhengzhou 450046, Peoples R China

3.Longhu Modern Immunol Lab, Zhengzhou 450002, Peoples R China

4.Peking Univ, Sch Adv Agr Sci, Beijing 100871, Peoples R China

5.Yangzhou Univ, Jiangsu Coinnovat Ctr Prevent & Control Important, Yangzhou 225009, Peoples R China

关键词： peptide-protein interaction; machine learning; random forest model; affinity; prediction

期刊名称：INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES （ 影响因子：5.6； 五年影响因子：6.2 ）

ISSN： 1661-6596

年卷期： 2023 年 24 卷 14 期

页码：

收录情况： SCI

摘要： The affinity of peptides is a crucial factor in studying peptide-protein interactions. Despite the development of various techniques to evaluate peptide-receptor affinity, the results may not always reflect the actual affinity of the peptides accurately. The current study provides a free tool to assess the actual peptide affinity based on virtual docking data. This study employed a dataset that combined actual peptide affinity information (active and inactive) and virtual peptide-receptor docking data, and different machine learning algorithms were utilized. Compared with the other algorithms, the random forest (RF) algorithm showed the best performance and was used in building three RF models using different numbers of significant features (four, three, and two). Further analysis revealed that the four-feature RF model achieved the highest Accuracy of 0.714 in classifying an independent unknown peptide dataset designed with the PEDV spike protein, and it also revealed overfitting problems in the other models. This four-feature RF model was used to evaluate peptide affinity by constructing the relationship between the actual affinity and the virtual docking scores of peptides to their receptors.

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