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.