High-Throughput MHC I Ligand Prediction Using MHCflurry

Abstract

MHCflurry is an open source package for peptide/MHC I binding affinity prediction. Its command-line and programmatic interfaces make it well-suited for integration into high-throughput bioinformatic pipelines. Users can download models fit to publicly available data or train predictors on their own affinity measurements or mass spec datasets. This chapter gives a tutorial on essential MHCflurry functionality, including generating predictions, training new models, and using the MHCflurry Python interface. MHCflurry is available at https://github.com/openvax/mhcflurry .

Keywords: Epitope prediction; HLA; Immunoinformatics; MHC; Neoantigen.