BindDM

Binding-Adaptive Diffusion Models for Structure-Based Drug Design

Official implementation for "Binding-Adaptive Diffusion Models for Structure-Based Drug Design" (AAAI 2024).

Affiliation: Tsinghua University, Peking University, University of Science and Technology of China, University of Chinese Academy of Sciences, ByteDance, Peng Cheng Laboratory.

Overview: BindDM extracts subcomplex from protein-ligand complex, and utilizes it to enhance the binding-adaptive 3D molecule generation in complex.

Environment

conda env create -f binddm.yaml
conda activate binddm

Data and Preparation

The data preparation follows TargetDiff. For more details, please refer to the repository of TargetDiff.

Training

python train.py

Sampling

python sample.py

Evaluation

python evaluate.py

Citation

@inproceedings{huang2024binddm,
  title={Binding-Adaptive Diffusion Models for Structure-Based Drug Design},
  author={Huang, Zhilin and Yang, Ling and Zhang, Zaixi and Zhou, Xiangxin and Bao, Yu and Zheng, Xiawu and Yang, Yuwei and Wang, Yu and Yang, Wenming},
  booktitle={The AAAI Conference on Artificial Intelligence},
  year={2024}
}