Machine learning optimization of peptides for presentation by class II MHCs

T cells play a critical role in normal immune responses to pathogens and cancer and can be targeted to MHC-presented antigens via interventions such as peptide vaccines. Here, we present a machine learning method to optimize the presentation of peptides by class II MHCs by modifying the peptides anchor residues. Our method first learns a model of peptide affinity for a class II MHC using an ensemble of deep residual networks, and then uses the model to propose anchor residue changes to improve peptide affinity. We use a high throughput yeast display assay to show that anchor residue optimization successfully improved peptide binding.