High-Throughput MHC I Ligand Prediction Using MHCflurry

Methods Mol Biol. 2020;2120:113-127. doi: 10.1007/978-1-0716-0327-7_8.


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.

MeSH terms

  • Computational Biology / methods
  • Histocompatibility Antigens Class I / metabolism*
  • Humans
  • Ligands
  • Peptides / chemistry
  • Peptides / metabolism*
  • Protein Binding
  • Software*


  • Histocompatibility Antigens Class I
  • Ligands
  • Peptides