tdc/

CYP3A4_Veith-Morgan

The CYP P450 genes are involved in the formation and breakdown (metabolism) of various molecules and chemicals within cells. Specifically, CYP3A4 is an important enzyme in the body, mainly found in the liver and in the intestine. It oxidizes small foreign organic molecules (xenobiotics), such as toxins or drugs, so that they can be removed from the body.

Binary classification. Given a drug SMILES string, predict CYP3A4 inhibition.

Total: 12,328 drugs

Install the following packages

pip install PyTDC
pip install DeepPurpose
pip install git+https://github.com/bp-kelley/descriptastorus
pip install dgl torch torchvision

You can also reference the colab notebook here

Random split on 70% training, 10% validation, and 20% testing

To load the dataset in TDC, type

Morgan chemical fingerprint with an MLP decoder. The model is tuned with 100 runs using the Ax platform.