Code for "IDL-PPBopt: A Strategy for Prediction and Optimization of Human Plasma Protein Binding of Compounds via an Interpretable Deep Learning Method"
That version of the model uses cuda.
- python 3.7
- pytorch 1.5.0
- openbabel 2.4.1
- rdkit
- scikit learn
- scipy
- cairosvg
Using conda:
1- Clone that repo.
2- Run the follwing command on the terminal inside the repo folder: conda env create -f environment.yml
To activate the conda environment run that command: conda activate IDL_PPBopt_cuda
The iPPB model was trained with AttentiveFP algorithm and saved in the "saved_models" file.
- Write the given molecules to input_compounds.csv file.
- Run IDL-PPBopt.ipynb in jupyter notebook.