Python 3.7x (may work with earlier versions, not tested)

Sklearn 0.0

Numpy 1.17.0

Pandas 1.2.3

Java environment

1.RankLib-2.16.jar(download)

train:

java -jar RankLib-2.16.jar -train train.txt   -ranker 0    -metric2t NDCG@50    -tree 500  -leaf 300  -shrinkage 0.03   
                           -mls 5   -tc 256 -save t_model.txt -out t_out.txt

test:

java -jar RankLib-2.16.jar -load t_model.txt -rank test.txt -indri test_rank.txt

2.index_available.py -- Get the index of the data that satisfies the constraint

3.AAF.py/SAF.py -- Extract features

MSE

CI

Rm2

The characteristics of drugs and proteins are obtained in the same way, and the code only lists one

Some data processing is done with linux commands,the code is simple, therefore the specific code is not listed.

sharing-sharing matrix --data processing.py

rm2 refers to the code in DeepDTA(Öztürk H, Özgür A, Ozkirimli E. DeepDTA: deep drug–target binding affinity prediction[J]. Bioinformatics, 2018, 34(17): i821-i829.)