IDL-PPBopt

Code for "IDL-PPBopt: A Strategy for Prediction and Optimization of Human Plasma Protein Binding of Compounds via an Interpretable Deep Learning Method"

Requirements

That version of the model uses cuda.

• python 3.7
• pytorch 1.5.0
• openbabel 2.4.1
• rdkit
• scikit learn
• scipy
• cairosvg

Installation

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

Model

The iPPB model was trained with AttentiveFP algorithm and saved in the "saved_models" file.

PPB prediction and second-level chemical rules' derivation for PPB optimization

1. Write the given molecules to input_compounds.csv file.
2. Run IDL-PPBopt.ipynb in jupyter notebook.