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docs: sync WET_LAB_HANDOFF and ROADMAP with 7-scaffold pool - #78
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WET_LAB_HANDOFF.md was still referencing "6 pilot panel seed families" after SEED-001 (magainin-1) was re-added as the 7th scaffold family in PR #72. This PR corrects all stale counts and adds missing coverage for the two newly relevant seeds. Changes: - "other 5 seeds" → "other 6 seeds" in SEED-006 special notes - Serum stability section heading and body updated: 6→7 families, 3→5 flagged families, SEED-001 and SEED-009 rows added to table - SEED-001 (score 0.49): natural magainin derivatives have documented serum t½ 15-30 min; model score may be accurate (not an underestimate); N-Ac/C-NH₂ modifications recommended in QC; D-Lys Wave 2 plan ready - SEED-009 (score 0.57): Pro-rich backbone resists protease cleavage 10-50× vs Lys/Arg-X bonds; model likely underestimates actual t½ - SEED-006 and SEED-007 stability range corrected (0.61-0.67 / 0.64-0.66) - Added SEED-001 (Magainin-1) Special Notes section: mechanism (carpet/ toroidal pore), novelty caveat (low — serves as positive control), synthesis guidance (N-Ac + C-NH₂ both recommended), assay interpretation matrix including what SEED-001 inactivity means ROADMAP.md: - External predictor row updated: tool list corrected (CAMPR4, AMPScanner, dbAMP, AntiCP2, Macrel), checklist status noted, Macrel v1.6.0 CLI ONNX bug documented (all sequences misclassified as NAMP; use web server)
HIGH: - Fix SEED-009 length contradiction: helix-wheel table showed "9 AA" while stability table (added this PR) correctly shows "12 AA"; aligned to 12 AA throughout (confirmed from pilot panel sequences) - SEED-009 stability row: replace unsupported "10-50x slower" kinetic claim with mechanistic explanation — Pro nitrogen lacks free H for serine protease oxyanion hole (Pro-X bonds uncleaved); X-Pro bonds hindered by cis-trans isomerisation (Vanhoof et al. 1995, FASEB J 9:736-744) MEDIUM: - SEED-001 mechanism: distinguish toroidal-pore (primary, NMR-supported; Matsuzaki 1996, Huang 2006) from carpet mechanism (secondary at high conc; Brogden 2005); add assay signature guidance to help distinguish in vitro - SEED-001 disagreement: document scorer conflict (activity=0.81 vs boman=0.43, disagreement=0.377) so wet-lab team can interpret potential inactivity - SEED-003 stability: remove Radzishevsky 2007 (lipopeptides, not relevant to conventional short AMPs); reframe as known model calibration limitation for <15 AA sequences LOW: - N-Ac/C-NH2 claim: remove unsupported "2-3x" multiplier; keep qualitative statement that modifications reduce exopeptidase exposure - ROADMAP: note AMPlify excluded due to GPU/ONNX env incompatibility
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Summary
WET_LAB_HANDOFF.md
New stability table rows:
ROADMAP.md
External predictor row corrected:
external_predict.py)Test plan
make test→ 1245 passed🤖 Generated with Claude Code