[cschanhniem]

Summary

Follow-up to PR #86 (novelty-check-broad). Updates documentation to reflect the key scientific findings from the 72-AMP broad novelty check.

Changes

ROADMAP.md

• Mark "True novelty check" as Partial (PR feat: novelty-check-broad — compare panel against 72-AMP curated database #86 covers curated 72-AMP DB; full APD3 BLASTp still needed before publication)
• Mark "Pre-registration of assay protocol" as Done (docs/ASSAY_PREREGISTRATION.md, PRs docs: add MRSA USA300 to preregistration, align serum stability protocol #83)

WET_LAB_PROBABILITY.md

• Correct SEED-003 mechanism description: was "bovine lactoferricin/defensin analogs" → now "RRWQWRMKKLG-class tachyplesin-like AMP (Tam 2002 J Biol Chem)" — corrected by broad novelty check finding 81.8% similarity to REF-RRW-001
• Raise SEED-003 P(MIC ≤ 16 µg/mL) from 50–65% → 60–75% because parent sequence RRWQWRMKKLG is a known-active AMP, elevating the prior
• Update composite P(panel zero hits): 0.000635 → 0.000508 reflecting corrected SEED-003 estimate
• Downgrade SEED-003 publishable novelty: 25–40% → 10–20% (limited novelty; SAR value is primary wet-lab benefit)
• Add cross-reference to NOVELTY_BROAD_CHECK.md in document header

Makefile

• Add novelty-broad target (depends on pilot)

Test plan

• Full test suite: 1277 passed (docs/Makefile changes have no code impact)

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