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docs: add SEED-003 Special Notes to WET_LAB_HANDOFF - #89
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SEED-003 variants were missing a dedicated special notes section despite being KNOWN_VARIANT (81.8% similar to RRWQWRMKKLG, a known-active AMP per PR #86 broad novelty check). Key additions: - Known-variant classification with implications for P(activity) (60-75%) and publication novelty (limited — value is as assay control) - Met oxidation risk warning for RRWNWRMKKMG at position 10 - Aggregation caution (Trp at >200 µM in aqueous buffer) - Scorer disagreement interpretation (0.23-0.26 = model consensus) - C-terminal amidation recommendation Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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….5.x - Version tag: v0.1.0 → v0.5.x (matches pipeline state) - Completed improvements: add PRs #71–#89 (face analysis, face segregation bonus AUROC 0.8420, wet-lab probability docs, novelty-check-broad, MRSA preregistration, EXPERT_REVIEW_PACK overhaul, WET_LAB_HANDOFF SEED-003 notes) - Bottom line: updated to post-PR #89; P(≥1 active MIC≤16) = 99.95% (P(zero) = 0.000508) from WET_LAB_PROBABILITY.md composite derivation - Broad novelty check paragraph: 16/20 NOVEL, 3 KNOWN_VARIANT, 1 CLOSE_RELATIVE; cross-reference to docs/NOVELTY_BROAD_CHECK.md - Stage 4 novelty table: SEED-003 annotated KNOWN_VARIANT (81.8% sim to RRWQWRMKKLG; raises P(active) 60–75%, lowers publication novelty 10–20%) - Stage 4 body: broad novelty check result block with classification thresholds - Highest-Probability Bets: SEED-003 row notes KNOWN_VARIANT status and updated per-family probability implications - Footer: generator version tag updated to v0.5.x
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…92) - DISCOVERY_PREDICTION.md: add PRs #90/#91 to completed-improvements line, update bottom-line tag post-PR #89 → post-PR #91 - WET_LAB_HANDOFF.md: add PROLINE_RICH_INTRACELLULAR / RPMI-1640 critical assay note to SEED-009 mechanism section; update assay matrix inactive guidance from "check MIC range" to "run RPMI-1640 parallel assay first" - RISK_REVIEW.md: extend high-proline-content row to mention PROLINE_RICH_INTRACELLULAR flag and RPMI-1640 recommendation (PR #90) - ASSAY_PREREGISTRATION.md + EXPERT_REVIEW_PACK.md: fix Krizsan et al. 2014 page citation 53:14546 → 53:12236 (correct DOI page) - Makefile: add `make help` target with one-line description for every pipeline target — improves discoverability for wet-lab handoff
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Summary
Adds a dedicated "SEED-003 Special Notes" section to
docs/WET_LAB_HANDOFF.md, which was missing one despite SEED-003 being one of the more nuanced candidates.Context
PR #86 (novelty-check-broad) established that SEED-003_VAR_017/012 are 81.8% similar to RRWQWRMKKLG (REF-RRW-001, tachyplesin-like known-active AMP, Tam 2002 J Biol Chem). This has important implications not previously documented in the wet-lab handoff.
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