DiffAlign: Diffusion-Based Molecular Alignment with Pocket-Aware Guidance

Official implementation of DiffAlign: Diffusion-Based Molecular Alignment with Pocket-Aware Guidance, accepted to Machine Learning in Structural Biology 2025.
Built on top of the GeoDiff codebase.

Setup

• Create the environment: conda create env -f env.yml
• Activate and install your extras as needed.

How to sample

• See alignment_example.ipynb for a runnable walkthrough using the provided pocket/query/reference structures.

License

MIT License (see LICENSE).

Contact

If you have any question, please contact me at iljung0810@hanyang.ac.kr.