Predicting MHC class I binder: existing approaches and a novel recurrent neural network solution

Abstract

Major histocompatibility complex (MHC) possesses important research value in the treatment of complex human diseases. A plethora of computational tools has been developed to predict MHC class I binders. Here, we comprehensively reviewed 27 up-to-date MHC I binding prediction tools developed over the last decade, thoroughly evaluating feature representation methods, prediction algorithms and model training strategies on a benchmark dataset from Immune Epitope Database. A common limitation was identified during the review that all existing tools can only handle a fixed peptide sequence length. To overcome this limitation, we developed a bilateral and variable long short-term memory (BVLSTM)-based approach, named BVLSTM-MHC. It is the first variable-length MHC class I binding predictor. In comparison to the 10 mainstream prediction tools on an independent validation dataset, BVLSTM-MHC achieved the best performance in six out of eight evaluated metrics. A web server based on the BVLSTM-MHC model was developed to enable accurate and efficient MHC class I binder prediction in human, mouse, macaque and chimpanzee.