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| Resource | Location | Description |
|---|---|---|
| 🧠 Pretrained model | model/ | Official NucleusDiff checkpoint |
| 🧬 Project data | data/ | Training, evaluation, and therapeutic-target artifacts |
| 💻 Implementation | GitHub | Source code, configuration, and usage instructions |
model/nucleusdiff_pretrained_model.pt — pretrained NucleusDiff checkpoint.data/crossdocked_v1.1_rmsd1.0_pocket10_processed_w_manifold_data_version.lmdb — preprocessed CrossDocked manifold dataset.data/crossdocked_pocket10_pose_w_manifold_data_split.pt — train/validation/test split used by NucleusDiff.data/crossdocked_v1.1_rmsd1.0.tar.gz — filtered CrossDocked data.data/split_by_name.pt — reference CrossDocked split.data/test_set.zip — protein test set used for docking evaluation.data/real_world.zip — therapeutic-target evaluation data.data/affinity_info.pkl — affinity metadata.data/test_vina_crossdock_dict.pkl — CrossDocked Vina evaluation metadata.pip install -U huggingface_hub1hf download LiangYan3612/NucleusDiff \
2 --include "model/*" \
3 --local-dir ./NucleusDiff_artifacts1hf download LiangYan3612/NucleusDiff \
2 --include "data/*" \
3 --local-dir ./NucleusDiff_artifacts1hf download LiangYan3612/NucleusDiff \
2 --local-dir ./NucleusDiff_artifacts1@article{liu2025manifold,
2 title={Manifold-constrained nucleus-level denoising diffusion model for structure-based drug design},
3 author={Liu, Shengchao and Yan, Liang and Du, Weitao and Liu, Weiyang and Li, Zhuoxinran and Guo, Hongyu and Borgs, Christian and Chayes, Jennifer and Anandkumar, Anima},
4 journal={Proceedings of the National Academy of Sciences},
5 volume={122},
6 number={41},
7 pages={e2415666122},
8 year={2025},
9 publisher={National Academy of Sciences}
10}