A simple pan-specific RNN model for predicting HLA-II binding peptides. (November 2021)

• Record Type: Journal Article
• Authors: Heng, Yu; Kuang, Zuyin; Xie, Wenzhao; Lan, Haoqi; Huang, Shuheng; Chen, Linxin; Shi, Tingting; Xu, Lei; Pan, Xianchao; Mei, Hu
• Is Part Of: Molecular immunology. Volume 139(2021)
• Page Start: 177
• Page End: 183
• Publication Date: 2021-11
• Subjects: Gated recurrent unit -- Recurrent neural network -- Human leukocyte antigen -- Peptide -- Prediction; Immunochemistry -- Periodicals; Molecular biology -- Periodicals; Immunochemistry -- Periodicals; Allergy and Immunology -- Periodicals; Molecular Biology -- Periodicals; Immunochimie -- Périodiques; Biologie moléculaire -- Périodiques; Immunochemistry; Molecular biology; Periodicals; Electronic journals; 571.96
• DOI: 10.1016/j.molimm.2021.09.004
• Languages: English
• ISSNs: 0161-5890

Abstract

Graphical abstract: Abstract: The prediction of human leukocyte antigen (HLA) class II binding peptides plays important roles in understanding the mechanism of immune recognition and developing effective epitope-based vaccines. In this work, gated recurrent unit (GRU)-based recurrent neural network (RNN) was successfully employed to establish a pan-specific prediction model of HLA-II-binding peptides by using only the HLA and peptide sequence information. In comparison with the existing pan-specific models of HLA-II-binding peptides, the GRU-based RNN model covered a broad spectrum of HLA-II molecules including 50 HLA-DR, 47 HLA-DQ, and 19 HLA-DP molecules with peptide lengths varying from 8 to 43 mers. The results demonstrated strong discriminant capabilities of the GRU-based RNN model, of which the AUC values were 0.92, 0.88, and 0.88 for the training, validation, and test sets, respectively. Also, the GRU-based model showed state-of-the-art performances in predicting the binding peptides with the length ranging from 8–32 mers, which provides an efficient method for predicting HLA-II-binding peptides of longer lengths in comparison with the available methods. Overall, taking the advantages of the RNN architecture, the established pan-specific GRU model can be used for predicting accurately the HLA-II-binding peptides in a simple and direct manner.