BioFormer

Efficiently predicting Drug Target Interaction

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Requirements

To install the TDC package, open the terminal and type:

pip install PyTDC

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Datasets

In the data folder, we provide all three processed datasets used in our model: BindingDB_Kd, KIBA, and DUDE. Besides drug smiles and protein sequence, we provide protein pdb as well as contactmap.

To prepare the datasets:

1. Download my_data.zip: https://drive.google.com/file/d/1fz8EZBOKFplIBugsX2eueR65ZHBBgEre/view?usp=sharing
2. Create a new folder my_data under data
3. Unzip my_data.zip in my_data

You should see the following data structure:

--data
----my_data
------my_data
--------bindingdb
--------dude
--------kiba

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Run

To train on kd, kiba or dude, simply run
bash train.sh [dataset], dataset is one of kd, kiba or dude
For example, train on kd, you should run:

bash train.sh kd

To view the logs while training, run bash view.sh [dataset]

bash view.sh kd