Epitope Prediction of Antigen Protein Using Attention-based LSTM Network

B-cells inducing antigen-specific immune responses in vivo produce large amounts of antigen-specific antibodies by recognizing the subregions (epitope regions) of antigen proteins. These antibodies can inhibit the functioning of antigen proteins. Predicting epitope regions is beneficial for the design and development of vaccines aimed to induce antigen-specific antibody production. However, prediction accuracy requires improvement. The conventional epitope region prediction methods have focused only on the target sequence in the amino acid sequences of an entire antigen protein and have not thoroughly considered its sequence and features as a whole. In the present paper, we propose a deep learning method based on long short-term memory with an attention mechanism to consider the characteristics of a whole antigen protein in addition to the target sequence. The proposed method achieves better accuracy compared with the conventional method in the experimental prediction of epitope regions using the data from the immune epitope database.