RPEMHC: improved prediction of MHC-peptide binding affinity by a deep learning approach based on residue-residue pair encoding
- paddle == 2.3.2
- python == 3.7
python preprocess.py ##before reproduction, several files need to be generated by preprocess.py
python train.py --mode cv ##5-flod cross-validation on IEDB2016
python train.py --mode lomo ##Leave one molecule out on IEDB2016
python train.py --mode binary_test ##independent test on Binary_test
python train.py --mode iC50_test ##independent test on IC50_test
python train.py --mode epitope ##independent test on T-cell epitope benchmark
python train.py --mode ablation ##ablation experiment
python train.py --mode binding_core ##binding core prediction
python train.py --mode seqlogo ##generate data to draw seq2logo
python train.py --mode CD4 ##evaluation compared with NetMHCIIpan-4.0
python train.py --mode CD8 ##evaluation compared with NetMHCpan-4.1
Trained models are provided in https://pan.quark.cn/s/2985aa5a6138