Improving MHC class I antigen-processing predictions using representation learning and cleavage site-specific kernels.

ABSTRACT: In this work, we propose a new deep-learning model, MHCrank, to predict the probability that a peptide will be processed for presentation by MHC class I molecules. We find that the performance of our model is significantly higher than that of two previously published baseline methods: MHCflurry and netMHCpan. This improvement arises from utilizing both cleavage site-specific kernels and learned embeddings for amino acids. By visualizing site-specific amino acid enrichment patterns, we observe that MHCrank's top-ranked peptides exhibit enrichments at biologically relevant positions and are consistent with previous work. Furthermore, the cosine similarity matrix derived from MHCrank's learned embeddings for amino acids correlates highly with physiochemical properties that have been experimen

SUBMITTER: Lawrence PJ 

PROVIDER: S-EPMC9499997 | biostudies-literature | 2022 Sep

REPOSITORIES: biostudies-literature