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ImmunePredictor is a pipeline developed in Python that predicts peptide cleavage, peptide-MHC affinity, stability, immunogenicity and self similarity (to human proteome) scores for human MHC class I.

The pipeline require the following external software tools:

  1. NetChop 3.1 - Download: - Note that we do not support the OSX version
  2. NetMHCpan 3.0 - Download:
  3. NetMHCstabpan 1.0 - Download:

Install and test:

  1. Download the "WP3-ImmunePredictor/src/", "WP3-ImmunePredictor/data/" and "WP3-ImmunoPredictor/test/" directories. Make sure that "src", "data" and "test" are located in the same directory.
  2. Download "data.tar.gz" from: Unpack the content into the "data" folder
  3. Install NetChop, NetMHCpan and NetMHCstabpan
  4. Open "WP3-ImmunePredictor/src/"
  5. In "", locate the "toolParams" class and set the absolute paths for the netChop, netMHCpan and netMHCstabpan binaries. Note that netChop also requires an environment directory


  1. Run "" to test the pipeline on an example input file from WP3-ImmunoPredictor/test/
  2. See "" for usage instructions