๐ง Work in progress...
The code has been tested in the following environment:
Package | Version |
---|---|
Python | 3.8.12 |
PyTorch | 1.10.1 |
CUDA | 11.3.1 |
PyTorch Geometric | 2.0.3 |
RDKit | 2020.09.5 |
OpenBabel | 3.1.0 |
conda env create -f env_cuda113.yml
conda activate SBDD-3D
conda create --name SBDD-3D python=3.8
conda activate SBDD-3D
conda install pytorch=1.10.1 torchvision torchaudio cudatoolkit=11.3 -c pytorch
conda install pyg -c pyg -c conda-forge
conda install easydict -c conda-forge
conda install rdkit openbabel python-lmdb -c conda-forge
conda install tensorboard -c conda-forge
Please refer to README.md
in the data
folder.
To sample molecules for the i-th pocket in the testset, please first download the trained models following
README.md
in the pretrained
folder. Then, run the following command:
python sample.py ./configs/sample.yml --data_id {i} # Replace {i} with the index of the data. i is between 0 and 99 for the testset.
๐ง Work in progress...
๐ง Work in progress...
@inproceedings{luo2021sbdd,
title={A 3D Generative Model for Structure-Based Drug Design},
author={Shitong Luo and Jiaqi Guan and Jianzhu Ma and Jian Peng},
booktitle={Thirty-Fifth Conference on Neural Information Processing Systems},
year={2021}
}