This repository is the official repository for BInD (Bond and Interaction generating Diffusion model)
conda create -n bindenv python=3.9 -y
conda activate bindenv
# ML
conda install scipy=1.11.3 numpy=1.26.0 pandas=2.1.1 scikit-learn=1.3.0 -y
conda install pytorch==1.11.0 cudatoolkit=11.3 -c pytorch -y
pip install torch-scatter==2.0.9 torch-sparse==0.6.15 torch-cluster==1.6.0 torch-geometric==2.1.0.post1 -f https://data.pyg.org/whl/torch-1.11.0+cu113.html
pip install tensorboard==2.15.1
# cheminformatics
pip install rdkit==2023.9.2
pip install biopython==1.81
conda install plip=2.3.0 -c conda-forge
conda install -c conda-forge openbabel==3.1.1
pip install meeko==0.1.dev3 scipy pdb2pqr vina==1.2.2
python -m pip install git+https://github.com/Valdes-Tresanco-MS/AutoDockTools_py3
git clone https://github.com/durrantlab/POVME
# posecheck
pip install prolif==2.0.3
git clone https://github.com/cch1999/posecheck.git
cd posecheck
pip install -e .
# utils
pip install pyyaml==6.0.1
pip install easydict==1.13
pip install parmap==1.7.0
# plots
pip install matplotlib==3.8.1
pip install seaborn==0.13.0| Data | Size | Path |
|---|---|---|
| Raw data | 1.7GB | data/raw/ |
| Processed data (whole) | 3.7GB | data/processed/ |
| Processed data (only test) | 3.3MB | data/processed/ |
| Data split keys | 3.3MB | data/ |
| POVME data | 0.7MB | data/ |
| Trained checkpoint | 10.7MB | save/ |
You can download the .tar.gz files provided above, extract them, and place the contents in the path.
Warning: Using --recreate parameter will overwrite the existing directory where training checkpoints are saved.
python process.py --recreate --save_dirn ./data/processed/my_data/ --raw_dirn ./data/raw/crossdocked_pocket10 To train BInD with the default settings, use the command below.
You can adjust the training configurations by editing the configs/train.yaml file.
For multi-GPU training, adjust the n_gpu and num_workers parameters as needed.
Additionally, setting the pre_load_dataset option to yes will load the dataset into memory in advance, reducing file I/O load.
Warning: Setting the save_dirn parameter will overwrite the existing directory where training checkpoints are saved.
python train.py configs/train.yamlpython generate_test_pockets.py configs/generate_test_pockets.yamlpython generate_single_pocket.py configs/generate_single_pocket.yaml@article{lee2025bind,
title={BInD: Bond and Interaction-Generating Diffusion Model for Multi-Objective Structure-Based Drug Design},
author={Lee, Joongwon and Zhung, Wonho and Seo, Jisu and Kim, Woo Youn},
journal={Advanced Science},
pages={e02702},
year={2025},
publisher={Wiley Online Library},
doi = {https://doi.org/10.1002/advs.202502702},
}
Lee, Joongwon |
Zhung, Wonho |
Seo, Jisu |