├── .gitignore ├── LICENSE ├── README.md ├── code ├── BerMol │ ├── bermol │ │ ├── __init__.py │ │ ├── dataloading.py │ │ ├── model.py │ │ ├── run.sh │ │ ├── tokenizer.py │ │ ├── trainer.py │ │ ├── utils.py │ │ └── vocab.py │ ├── requirements.txt │ ├── run.sh │ ├── scripts │ │ └── featurize.py │ └── setup.py ├── data_prepare.sh ├── data_process │ ├── data_split_dta.py │ ├── data_split_dti.py │ ├── data_split_moa.py │ └── extract_feature.py ├── test.sh ├── training_validation.py └── utils.py ├── data ├── docking │ └── cdk6 │ │ ├── 5l2i_Palbociclib.pdb │ │ ├── Axitinib_out.pdbqt │ │ ├── Canertinib_dihydrochloride_out.pdbqt │ │ ├── Doramapimod_out.pdbqt │ │ ├── Granisetron_out.pdbqt │ │ └── Mubritinib_out.pdbqt ├── dta │ ├── davis │ │ ├── Y │ │ ├── ligands_can.txt │ │ └── proteins.txt │ └── kiba │ │ ├── Y │ │ ├── ligands_can.txt │ │ └── proteins.txt ├── dti │ ├── hetionet │ │ ├── drug_smiles.csv │ │ ├── dti.csv │ │ ├── fp.txt │ │ ├── kg.csv.zip │ │ ├── pro_ctd.txt │ │ └── protein_seq.csv │ └── yamanishi_08 │ │ ├── drug_smiles.csv │ │ ├── dti.csv │ │ ├── fp.txt │ │ ├── kg.csv │ │ ├── pro_ctd.txt │ │ └── protein_seq.csv └── moa │ ├── activation │ ├── drug_smi.csv │ ├── dti.csv │ ├── tar_gene.csv │ └── tar_seq.csv │ └── inhibition │ ├── drug_smi.csv │ ├── dti.csv │ ├── tar_gene.csv │ └── tar_seq.csv ├── img ├── flowchart.pdf └── flowchart.png └── requirements.txt /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSUBioGroup/DTIAM/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSUBioGroup/DTIAM/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 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