| CupOFMoCA — PROTAC release |
| Copyright 2026 CupOFMoCA authors |
|
|
| The first-party code in this release is licensed under Apache License 2.0; see |
| LICENSE. Model weights and third-party downloads are subject to their own terms, |
| which users are responsible for reviewing. |
|
|
| Redistributed third-party code |
| |
|
|
| src/defog/ |
| DeFoG, https://github.com/manuelmlmadeira/DeFoG |
| MIT License, reproduced at src/defog/LICENSE. |
| src/defog/src/datasets/protac_dataset.py is a first-party addition. |
| The upstream graph-benchmark evaluation helpers under |
| src/defog/src/analysis/orca/ are NOT redistributed: that C++ code carries no |
| license header and is unused by the PROTAC pipeline. |
|
|
| Third-party code that is NOT redistributed |
| |
|
|
| Two optional components are published by their authors without any license |
| file, so this release cannot lawfully redistribute them. Run |
| `python scripts/fetch_third_party.py` to obtain them from their upstream |
| repositories at the commits used for the paper, and review the upstream terms |
| before use. |
|
|
| DegradeMaster https://github.com/ABILiLab/DegradeMaster |
| pinned commit aa149beaf067a051e070b3b281f7dba43c2f3e90 |
| Needed only for predicted-degradation scoring. |
|
|
| EGFR-PROPK https://github.com/Zhang-Ran-0119/EGFR-PROPK |
| pinned commit 6940cb90c449e6c6d0678508fc2f228da796e028 |
| Needed only for the EGFR-only PK columns of batch_report.py. |
|
|
| Linker generation with scripts/generate.py does not require either component. |
|
|
| Derived data |
| |
|
|
| The PROTAC-DB derived tables (data/linker.csv) and the target and E3 pocket |
| graphs used for degradation scoring were prepared by the CupOFMoCA authors from |
| publicly available sources: PROTAC-DB (Weng et al., Nucleic Acids Research 2021) |
| and the RCSB Protein Data Bank. The fine-tuned generator checkpoint under |
| checkpoints/ is a derivative of the released DeFoG GuacaMol checkpoint and |
| inherits its MIT terms. |
|
|
