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LNG_UB_LIGASE_UNIT: a ubiquitination does not deplete its own ligase (deltasignal specs/089), default on - #122
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… deplete its own ligase - a leaf of the curated activeUnit, or of a complex released unchanged, that leaves the reaction unmodified is not the substrate; default off Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
…dam 2026-10-22: tuning +22, experimental +3, held-out -2 traced) Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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The ubiquitin pass took every input leaf whose gene is also in the output as the substrate, so a ligase carried through unchanged drained its own free subunits (CKS1B under SCF(Skp2), SMURF1/2 under SMAD7 and PTCH1 complexes, STUB1, RNF111, TRIM33, ITCH...).
Now a leaf of the catalyst's curated
activeUnit, or of a complex released unchanged (where no activeUnit is curated), is not the substrate when it leaves the reaction unmodified. Autoubiquitination and the substrate's partners (EGFR and GRB2 under CBL, the specs/078 loss) are untouched.variant_pooledges no longer needed; nothing else changes (build20261022-1541_d31f95e_ulu).ulu: tuning +22 (p 0.0001), experimental +3, held-out −2 (p 0.63, each loss traced in deltasignal specs/089 research.md). Adopted by Adam, 2026-10-22.tests/test_ub_ligase_unit.py(the substrate rule, and the whole pass against a stubbed graph, on and off). The one failing local test is the stale-outputtest_main_edges_proportional_to_best_matches[...983169], which fails on main too.Needs your review to merge (branch protection). After the merge I rebuild the canonical catalog from main.
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