Peptide-MHC binding affinity prediction
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
scripts/train-class1-allele-specific-models.py
This will train separate models for each HLA type.
from mhcflurry import Mhc1BindingPredictor
predictor = Mhc1BindingPredictor('A0201')
predictor.predict_peptides(['SIINFEKL']) Allele Peptide Prediction
0 A0201 SIINFEKL 586.730529