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HTTP/2 301 server: GitHub.com content-type: text/html location: https://yanliang3612.github.io/NucleusDiff/ access-control-allow-origin: * strict-transport-security: max-age=31556952 expires: Tue, 30 Dec 2025 04:54:30 GMT cache-control: max-age=600 x-proxy-cache: MISS x-github-request-id: 48B7:2685F2:986443:AB5E03:695358AE accept-ranges: bytes age: 0 date: Tue, 30 Dec 2025 04:44:30 GMT via: 1.1 varnish x-served-by: cache-bom-vanm7210045-BOM x-cache: MISS x-cache-hits: 0 x-timer: S1767069870.006535,VS0,VE223 vary: Accept-Encoding x-fastly-request-id: 1c3f42e904879f689fe308b01bda963850e80bc5 content-length: 162 HTTP/2 200 server: GitHub.com content-type: text/html; charset=utf-8 last-modified: Wed, 29 Oct 2025 05:52:17 GMT access-control-allow-origin: * strict-transport-security: max-age=31556952 etag: W/"6901ab91-1f4c" expires: Tue, 30 Dec 2025 04:54:30 GMT cache-control: max-age=600 content-encoding: gzip x-proxy-cache: MISS x-github-request-id: E10D:2685F2:986444:AB5E08:695358AD accept-ranges: bytes age: 0 date: Tue, 30 Dec 2025 04:44:30 GMT via: 1.1 varnish x-served-by: cache-bom-vanm7210045-BOM x-cache: MISS x-cache-hits: 0 x-timer: S1767069870.243565,VS0,VE209 vary: Accept-Encoding x-fastly-request-id: 64a87d8bbd2fac4882ecc3fbbf0a876aa5bad4f0 content-length: 2110 NucleusDiff

Manifold-Constrained Nucleus-Level Denoising Diffusion Model for Structure-Based Drug Design
Proceedings of the National Academy of Sciences 2025

¹Caltech
²UC Berkeley
³Alibaba DAMO Academy
⁴Max Planck Institute for Intelligent Systems
⁵University of Toronto
⁶University of Ottawa

^♠Equal contribution
^♦Equal advising

NucleusDiff Pipeline

Atom Collision in Structure-Based Drug Design

Inference

Concurrent Visualization of Ligand-Specific and Joint Ligand-Manifold Inference Processes in NucleusDiff: Comparative Analysis of the Evolution from Random Noise to Final Structures across Proteins 2NGS and 4U5S.

Citation

@misc{liu2024manifoldconstrainednucleusleveldenoisingdiffusion,
      title={Manifold-Constrained Nucleus-Level Denoising Diffusion Model for Structure-Based Drug Design}, 
      author={Shengchao Liu and Divin Yan and Weitao Du and Weiyang Liu and Zhuoxinran Li and Hongyu Guo and Christian Borgs and Jennifer Chayes and Anima Anandkumar},
      year={2024},
      eprint={2409.10584},
      archivePrefix={arXiv},
      primaryClass={q-bio.QM},
      url={https://arxiv.org/abs/2409.10584}, 
}

Original Source | Taken Source

Manifold-Constrained Nucleus-Level Denoising Diffusion Model for Structure-Based Drug Design
Proceedings of the National Academy of Sciences 2025

Paper

Code

NucleusDiff Pipeline

Atom Collision in Structure-Based Drug Design

Inference

Concurrent Visualization of Ligand-Specific and Joint Ligand-Manifold Inference Processes in NucleusDiff: Comparative Analysis of the Evolution from Random Noise to Final Structures across Proteins 2NGS and 4U5S.

Citation

Manifold-Constrained Nucleus-Level Denoising Diffusion Model for Structure-Based Drug Design Proceedings of the National Academy of Sciences 2025

Paper

Code

NucleusDiff Pipeline

Atom Collision in Structure-Based Drug Design

Inference

Concurrent Visualization of Ligand-Specific and Joint Ligand-Manifold Inference Processes in NucleusDiff: Comparative Analysis of the Evolution from Random Noise to Final Structures across Proteins 2NGS and 4U5S.

Citation

Manifold-Constrained Nucleus-Level Denoising Diffusion Model for Structure-Based Drug Design
Proceedings of the National Academy of Sciences 2025