ET-Score

A scoring function based on Extra Trees algorithm for predicting ligand-protein binding affinity. PDBbind 2016v refined set minus core set is used for training ET-Score and core set is used as an independent test set.

Contact

Milad Rayka, [email protected]

Citation

ET-score: Improving Protein-ligand Binding Affinity Prediction Based on Distance-weighted Interatomic Contact Features Using Extremely Randomized Trees Algorithm

Installation

Below packages should be installed for using ET-Score. Dependecies:

• python >= 3.7.0
• numpy
• scipy
• pandas
• biopandas >= 0.2.4
• joblib
• scikit-learn

For installing first make a virtual environment and activate it.

On windows:

   python py -m venv env
   .\env\Scripts\activate

On macOS and Linux:

   python3 -m venv env
   source env/bin/activate

Which env is the location to create the virtual environment. Now you can install packages:

   pip install *package_name*

Usage

1- Preparing ligand and protein file

a- Ligand and protein structure should be saved in .mol2 and .pdb format files respectively.
b- Each ligand and protein files for a specific complex must be placed in a same folder.

for example:

    ./1a1e/1a1e_ligand.mol2
    ./1a1e/1a1e_protein.pdb
    ./1a4k/1a4k_ligand.mol2
    ./1a4k/1a4k_protein.pdb

2- Generating features

generate_feature.py is used for generating features of ET-Score:

   python generate_feature.py -h  
   python generate_feature.py -d file_directory  

3- Training Random Forest(RF) of Extra Trees(ET) based on generated features

train_test.p script is used for optimizing hyperparameters(max_features), training(both RF and ET) and predicting for a test set. -y flag lets the script to optimize hyperparameters.

   python train_test.py -h
   python train_test.py features_file.xlsx test_list_file.txt binding_affinity_file.xlsx -y True

4- Use a trained model for predicting pKd values for new samples

If you don't want to train your model, you can simply use et_score.sav which is our best trained model or ET-Score (Download from FigShare). For doing thi task predict.py should be used. Hydrogens should be added to both ligands and proteins.

   python predict.py -h
   python predict.py -m et_score.sav -d file_directory