High-Throughput MHC I Ligand Prediction Using MHCflurry

  • Timothy O’DonnellEmail author
  • Alex Rubinsteyn
Part of the Methods in Molecular Biology book series (MIMB, volume 2120)


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

Key words

Epitope prediction MHC HLA Neoantigen Immunoinformatics 


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2020

Authors and Affiliations

  1. 1.Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkUSA

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