# Third-party provenance and rights status

This release preserves existing research inputs and outputs. The author confirmed the applicable redistribution terms on 2026-10-31 and authorized this GitHub publication; see the [confirmation record](../provenance/author_redistribution_confirmation.json). **No new blanket license is assigned to third-party data or models.** The source checks below record the evidence available during preparation and historical identifier limits; they do not replace component-specific terms.

| Component | Verified source/evidence | Terms and historical provenance notes |
|---|---|---|
| Project original software and software documentation | The authors selected the [MIT License](../LICENSE_CODE), copyright 2026 Sean Wan, Jiabao Brad Wang, Mustafa Misir. Scope is defined in [NOTICE.md](../NOTICE.md). | Preserve the copyright and permission notice. This software license does not cover datasets, research results, embeddings, model weights, the manuscript, or figures. |
| Upstream MolAS code | [Official repository](https://github.com/BradWangW/MolAS) and [LICENSE](https://github.com/BradWangW/MolAS/blob/main/LICENSE): MIT, copyright 2025 Jiabao Brad Wang, covering software and associated documentation. | Preserve the MIT notice if copying covered code. It does not establish a license for separately hosted data. |
| Recovered historical `MolAS_AL-main` software | The original downloaded source includes its own MIT `LICENSE`, preserved in `code/downstream/historical_molas/` with a content manifest. | Preserve that notice. The unversioned source snapshot and launcher settings do not independently establish every historical run configuration or a blanket dataset license. |
| Processed MolAS data/checkpoints | MolAS README and [published article](https://link.springer.com/article/10.1186/s13321-026-01168-8) identify [Zenodo record 17760688](https://zenodo.org/records/17760688). | Automated preparation checks could not independently retrieve the dataset license: record/API requests failed and the DataCite request returned 403. The author subsequently confirmed the applicable terms. No new MIT or CC BY dataset label is inferred from software/article licensing. |
| MOAD-derived complex selection and annotations | [Original authors' final update](https://doi.org/10.1038/s41598-023-29996-w). | Preserve source/version/curation information and the applicable terms confirmed by the author for the actual acquired files. The current bindingmoad.org domain is not reliable evidence of the historical dataset terms. |
| PDB archive structural files | [RCSB policies](https://www.rcsb.org/pages/policies) state that PDB archive data are under CC0. | This does not extend automatically to externally integrated resources, processed annotations, docking outputs, model weights, or every file in a mixed archive. RCSB explicitly distinguishes external-provider terms. |
| ESM-C protein graphs | The [preserved generator](../code/downstream/historical_molas/embedding_generation/data/pdb_processor.py) requests `ESMC.from_pretrained("esmc_600m")`. The official [`biohub/esmc-600m-2024-12` model card at revision `e4d83bc`](https://huggingface.co/biohub/esmc-600m-2024-12/blob/e4d83bc7e10fd55c92e598e545f4a76bf04a6e5c/README.md) states MIT and notes that dependencies may have other licenses. | The historical source does not pin the weights revision. The verified current model terms do not by themselves identify the exact historical weights or establish a license for the mixed graph dataset. Preserve applicable notices. The author confirmed release terms; the exact historical weights revision remains unpinned. |
| ChemBERTa ligand embeddings | The [preserved ligand notebook](../code/downstream/historical_molas/embedding_generation/ligand_chemberta_generation.ipynb) loads a local directory named `chemberta_77M_MLM`, consistent with the identifier [`DeepChem/ChemBERTa-77M-MLM`](https://huggingface.co/DeepChem/ChemBERTa-77M-MLM/tree/main). | The exact historical model/revision cannot be established from this local directory name. Automated source checks found no model card or license file in the inspected repository tree. The author subsequently confirmed release terms; this record does not infer a license from another ChemBERTa variant or the MolAS code license. |
| Combined feature cache | The original normalization/projection code and successful source-to-cache comparison are documented in the [data card](data_card.md). The existing cache and its verified row mapping are preserved. | Verifying the transformation and numerical identity does not assign new terms to the source embeddings or derived dataset. The author confirmed input-artifact redistribution terms separately from the MIT license covering project software. |
| AL docking score/runtime tables and derived results | Local source files, explicit recovery records, and SHA-256 manifests. | The author confirmed the applicable redistribution terms and authorized these archived results in the GitHub release. A separate dataset license label is not invented. |
| New packaging/validation/preparation utilities | Created for this local release-preparation task and covered by the authors' selected [MIT License](../LICENSE_CODE). | Preserve the copyright and permission notice; third-party components retain their own terms. |

The upstream website and official documentation were checked on 2026-10-31. The subsequent author confirmation resolves the publication authorization for this GitHub release. Historical model revisions and missing independently retrieved license documents remain recorded as provenance limits, rather than current requests for permission. The project's MIT license applies to its original software; the separate dataset release should state its actual component terms. The [Hugging Face license documentation](https://huggingface.co/docs/hub/repositories-licenses) describes metadata and does not assign a license to source material.

The large structural graph inputs are included in this HF upload payload. Author-owned data contributions have the CC BY 4.0 grant in LICENSE_DATA.md; third-party components retain their source terms. Record the actual Hub revision after publication.


HF-specific license scope and delegated selection are recorded in `../provenance/hf_release_authorization.json`; the original GitHub confirmation remains historical evidence.