DeepMHCII

DeepMHCII: A Novel Binding Core-Aware Deep Interaction Model for Accurate MHC II-peptide Binding Affinity Prediction

Requirements

• python==3.9.7
• pytorch==1.10.2
• numpy==1.21.2
• scipy==1.7.3
• scikit-learn==1.0.2
• click==8.0.4
• ruamel.yaml==0.16.12
• tqdm==4.62.3
• logzero==1.7.0

Experiments

python main.py -d configure/data.yaml -m configure/deepmhcii.yaml # train and evaluation on independent test set.
python main.py -d configure/data.yaml -m configure/deepmhcii.yaml --mode 5cv # 5 cross-validation
python main.py -d configure/data.yaml -m configure/deepmhcii.yaml --mode lomo # leave one molecule out cross-validation
python main.py -d configure/data.yaml -m configure/deepmhcii.yaml --mode binding # binding core prediction (after model training)
python main.py -d configure/data.yaml -m configure/deepmhcii.yaml --mode seq2logo -a <allele> # seq2logo

Declaration

It is free for non-commercial use. For commercial use, please contact Mr. Ronghi You and Prof. Shanfeng Zhu (zhusf@fudan.edu.cn).