arahuja/mhcflurry

Peptide-MHC binding affinity prediction

mhcflurry

Peptide-MHC binding affinity prediction

Quickstart

Set up the Python environment:

# (set up environment)
pip install scipy Cython
pip install h5py
python setup.py develop

Download, Normalize, and Combine Training Data:

(make sure you have wget available, e.g. brew install wget on Mac OS X)

scripts/download-iedb.sh
scripts/download-peters-2013-dataset.sh
scripts/create-iedb-class1-dataset.py
scripts/create-combined-class1-dataset.py

Train Neural Network Models

scripts/train-class1-allele-specific-models.py

This will train separate models for each HLA type.

Making predictions

from mhcflurry import Mhc1BindingPredictor
predictor = Mhc1BindingPredictor('A0201')
predictor.predict_peptides(['SIINFEKL'])

  Allele   Peptide  Prediction
0  A0201  SIINFEKL  586.730529