cschanhniem · Jun 28, 2026 · Jun 28, 2026 · Jun 28, 2026
diff --git a/docs/DISCOVERY_PREDICTION.md b/docs/DISCOVERY_PREDICTION.md
@@ -3,7 +3,7 @@
 **Pipeline:** OpenAMP-Foundry v0.5.x  
 **Date:** 2026-06-28 (updated 2026-06-28)  
 **Status:** Pre-synthesis scientific assessment — for expert review before ordering  
-**Completed improvements:** Serum stability scoring (PR #31/#32), Family diversity cap (PR #31), Reference set expansion 44→73 sequences (PR #33), Net charge pH 7.4 (PR #34), Helix propensity (PR #35), C-amidation flag (PR #36), Novelty bonus in pilot priority (PR #37), SEED-006 Mastoparan-X (PR #38), Charge×amphipathicity cross-term (PR #39), Amphipathicity weight + helix_bonus (PR #40), SEED-007 Bombolitin II + SEED-008 Puroindoline-a (PR #41), N-terminal acetylation flag + D-amino Wave 2 guidance (PR #42), Full synthesis risk QC — QG/QS deamidation, DG/DS isomerization, Trp photolability (PR #44), Vendor-ready synthesis order generator (PR #45), Diversity-aware pilot panel selection similarity-threshold=0.75 (PR #46), Selectivity proxy + HIGH_CYTOTOX_RISK flag — charge/GRAVY-based mammalian cytotoxicity risk detector (PR #47), selectivity_proxy routed into pilot_priority formula — low-cytotox-risk candidates gently demoted (PR #48), Elastase resistance (HNE 3-protease stability model) + aggregation propensity scoring (synthesis feasibility penalty) (PR #49), Aggregation-safe mutation generation + balanced K/R charge variants + SynthQC continuous aggregation score (PR #50), Proline synthesis penalty + helix bonus enhancement — AUROC 0.8138 → 0.8164 (PR #51), Safety pH74 charge consistency + stronger cytotoxicity penalty — SEED-004 net selectivity swing increased 0.035→0.055 (PR #53), AUPRC metric + SEED-009 (Bac2A proline-rich) + SEED-010 (KR-12 LL-37 fragment) (PR #58), ATCC strain corrections + preregistration assay protocol + negative result schema (PR #60), **CRITICAL FIX: SEED-008 Trp-rich scaffold reinstated in synthesis pool (was excluded by Boman W scale artifact); all 10 seeds generated; SEED-007/009 newly included; SEED-004 correctly excluded by safety gate; 6 mechanism-diverse scaffolds confirmed in synthesis pool** (PR #61), Phase3.yaml AUROC documented (0.7936→0.7890 after PR #65) (PR #63), Stale threshold/reference-count docs corrected (PR #64), **Trp-weighted aromatic bonus (1.5× Trp vs Phe/Tyr; Wimley-White interfacial mechanism); safety abs() bug fix (negative charge does not cause hemolysis); Eisenberg scale comment fix; pool SEED-006: 11→10, SEED-009: 18→19; AUROC 0.8164→0.8086** (PR #65), **Duplicate validation entry removed (REF-GIG-001 = magainin-2 = REF-MAG-001 counted twice); corrected AUROC 0.8086→0.8047 (pipeline), 0.7890→0.7846 (phase3); 43-AMP + 44-background set (n=87)** (PR #66), **Windowed hydrophobic moment (window=11, Eisenberg standard) replaces full-sequence mu_h for activity scoring; anionic guard (charge_density_ph74 < 0.0 → score 0.0); Python eager-eval bug fix in feature dict fallback; 23 new tests; AUROC 0.8047→0.8348 (pipeline), 0.7846→0.8126 (phase3)** (PR #70), Rotation-invariant helix-wheel face analysis — identifies non-helical mechanism class pre-synthesis (PR #71), **Face segregation bonus (helix_wheel_amphipathic_score × 0.05) in activity_likeness_score; max_disagreement raised 0.40→0.45 for SEED-008 Trp-rich class; AUROC 0.8348→0.8420, bootstrap CI₉₅: 0.76–0.91** (PR #72), Lab_results dir loading + toxicity flag branch coverage (PR #80), **Wet-lab probability analysis (WET_LAB_PROBABILITY.md) + gold-standard calibration + ASSAY_PREREGISTRATION.md with MRSA USA300 and serum stability gate** (PR #81/#83), SEED-007 helix-wheel length fix 18 AA→11 AA (PR #84), CLI integration tests — gold-standard, external-predict, pilot-confident, diversity-check; 7-seed pool documentation sync (PRs #74–#79/#82/#85), **novelty-check-broad CLI + 72-AMP broad novelty check: 16/20 NOVEL, 3 KNOWN_VARIANT (SEED-003 variants at 81.8% similarity to RRWQWRMKKLG = tachyplesin-like Tam 2002 J Biol Chem), 1 CLOSE_RELATIVE; docs/NOVELTY_BROAD_CHECK.md generated** (PR #86), **WET_LAB_PROBABILITY.md updated: SEED-003 mechanism corrected to RRWQWRMKKLG-class, P(MIC≤16) raised 50–65%→60–75%, novelty for publication lowered 25–40%→10–20%; composite P(≥1 active MIC≤16) = 99.95% (P(zero) = 0.000508)** (PR #87), **EXPERT_REVIEW_PACK.md overhauled: v0.5.x state, 7-seed mechanism table, full 20-candidate novelty table, SEED-008/009 mechanism notes, Melittin safety blind spot** (PR #88), WET_LAB_HANDOFF SEED-003 Special Notes: KNOWN_VARIANT classification (wet-lab SAR value retained), Met oxidation risk, aggregation caution, C-terminal amidation recommendation (PR #89), PROLINE_RICH_INTRACELLULAR flag in presynth QC — RPMI-1640 parallel assay recommendation for ≥25% Pro sequences; all four SEED-009 pilot variants flagged (Krizsan et al. 2014 Angew Chem Int Ed 53:12236) (PR #90), amphipathic_score (helix_wheel_amphipathic_score) and charge_ph74 (net_charge_ph74 at pH 7.4) added to pilot panel CSV output for wet-lab within-family prioritization (PR #91), Doc sync: Krizsan citation 53:14546→53:12236, RPMI-1640 note added to WET_LAB_HANDOFF SEED-009 section, RISK_REVIEW.md PROLINE_RICH_INTRACELLULAR note, make help target (PR #92), ROADMAP v0.7.x section documents PRs #73–#92 wet-lab readiness package (PR #93), 5 tests covering LONG_PEPTIDE flag, no-flags checklist branch, and length-filter failure mode — 1292 tests passing 96% coverage (PR #94), His pKa unified 6.0→6.5 (Bjellqvist 1993) across presynth_check.py and physchem.py, METHODS.md safety abs() correction, ensemble.py docstring with config weight references (PR #95)
+**Completed improvements:** Serum stability scoring (PR #31/#32), Family diversity cap (PR #31), Reference set expansion 44→73 sequences (PR #33), Net charge pH 7.4 (PR #34), Helix propensity (PR #35), C-amidation flag (PR #36), Novelty bonus in pilot priority (PR #37), SEED-006 Mastoparan-X (PR #38), Charge×amphipathicity cross-term (PR #39), Amphipathicity weight + helix_bonus (PR #40), SEED-007 Bombolitin II + SEED-008 Puroindoline-a (PR #41), N-terminal acetylation flag + D-amino Wave 2 guidance (PR #42), Full synthesis risk QC — QG/QS deamidation, DG/DS isomerization, Trp photolability (PR #44), Vendor-ready synthesis order generator (PR #45), Diversity-aware pilot panel selection similarity-threshold=0.75 (PR #46), Selectivity proxy + HIGH_CYTOTOX_RISK flag — charge/GRAVY-based mammalian cytotoxicity risk detector (PR #47), selectivity_proxy routed into pilot_priority formula — low-cytotox-risk candidates gently demoted (PR #48), Elastase resistance (HNE 3-protease stability model) + aggregation propensity scoring (synthesis feasibility penalty) (PR #49), Aggregation-safe mutation generation + balanced K/R charge variants + SynthQC continuous aggregation score (PR #50), Proline synthesis penalty + helix bonus enhancement — AUROC 0.8138 → 0.8164 (PR #51), Safety pH74 charge consistency + stronger cytotoxicity penalty — SEED-004 net selectivity swing increased 0.035→0.055 (PR #53), AUPRC metric + SEED-009 (Bac2A proline-rich) + SEED-010 (KR-12 LL-37 fragment) (PR #58), ATCC strain corrections + preregistration assay protocol + negative result schema (PR #60), **CRITICAL FIX: SEED-008 Trp-rich scaffold reinstated in synthesis pool (was excluded by Boman W scale artifact); all 10 seeds generated; SEED-007/009 newly included; SEED-004 correctly excluded by safety gate; 6 mechanism-diverse scaffolds confirmed in synthesis pool** (PR #61), Phase3.yaml AUROC documented (0.7936→0.7890 after PR #65) (PR #63), Stale threshold/reference-count docs corrected (PR #64), **Trp-weighted aromatic bonus (1.5× Trp vs Phe/Tyr; Wimley-White interfacial mechanism); safety abs() bug fix (negative charge does not cause hemolysis); Eisenberg scale comment fix; pool SEED-006: 11→10, SEED-009: 18→19; AUROC 0.8164→0.8086** (PR #65), **Duplicate validation entry removed (REF-GIG-001 = magainin-2 = REF-MAG-001 counted twice); corrected AUROC 0.8086→0.8047 (pipeline), 0.7890→0.7846 (phase3); 43-AMP + 44-background set (n=87)** (PR #66), **Windowed hydrophobic moment (window=11, Eisenberg standard) replaces full-sequence mu_h for activity scoring; anionic guard (charge_density_ph74 < 0.0 → score 0.0); Python eager-eval bug fix in feature dict fallback; 23 new tests; AUROC 0.8047→0.8348 (pipeline), 0.7846→0.8126 (phase3)** (PR #70), Rotation-invariant helix-wheel face analysis — identifies non-helical mechanism class pre-synthesis (PR #71), **Face segregation bonus (helix_wheel_amphipathic_score × 0.05) in activity_likeness_score; max_disagreement raised 0.40→0.45 for SEED-008 Trp-rich class; AUROC 0.8348→0.8420, bootstrap CI₉₅: 0.76–0.91** (PR #72), Lab_results dir loading + toxicity flag branch coverage (PR #80), **Wet-lab probability analysis (WET_LAB_PROBABILITY.md) + gold-standard calibration + ASSAY_PREREGISTRATION.md with MRSA USA300 and serum stability gate** (PR #81/#83), SEED-007 helix-wheel length fix 18 AA→11 AA (PR #84), CLI integration tests — gold-standard, external-predict, pilot-confident, diversity-check; 7-seed pool documentation sync (PRs #74–#79/#82/#85), **novelty-check-broad CLI + 72-AMP broad novelty check: 16/20 NOVEL, 3 KNOWN_VARIANT (SEED-003 variants at 81.8% similarity to RRWQWRMKKLG = tachyplesin-like Tam 2002 J Biol Chem), 1 CLOSE_RELATIVE; docs/NOVELTY_BROAD_CHECK.md generated** (PR #86), **WET_LAB_PROBABILITY.md updated: SEED-003 mechanism corrected to RRWQWRMKKLG-class, P(MIC≤16) raised 50–65%→60–75%, novelty for publication lowered 25–40%→10–20%; composite P(≥1 active MIC≤16) = 99.95% (P(zero) = 0.000508)** (PR #87), **EXPERT_REVIEW_PACK.md overhauled: v0.5.x state, 7-seed mechanism table, full 20-candidate novelty table, SEED-008/009 mechanism notes, Melittin safety blind spot** (PR #88), WET_LAB_HANDOFF SEED-003 Special Notes: KNOWN_VARIANT classification (wet-lab SAR value retained), Met oxidation risk, aggregation caution, C-terminal amidation recommendation (PR #89), PROLINE_RICH_INTRACELLULAR flag in presynth QC — RPMI-1640 parallel assay recommendation for ≥25% Pro sequences; all four SEED-009 pilot variants flagged (Krizsan et al. 2014 Angew Chem Int Ed 53:12236) (PR #90), amphipathic_score (helix_wheel_amphipathic_score) and charge_ph74 (net_charge_ph74 at pH 7.4) added to pilot panel CSV output for wet-lab within-family prioritization (PR #91), Doc sync: Krizsan citation 53:14546→53:12236, RPMI-1640 note added to WET_LAB_HANDOFF SEED-009 section, RISK_REVIEW.md PROLINE_RICH_INTRACELLULAR note, make help target (PR #92), ROADMAP v0.7.x section documents PRs #73–#92 wet-lab readiness package (PR #93), 5 tests covering LONG_PEPTIDE flag, no-flags checklist branch, and length-filter failure mode — 1292 tests passing 96% coverage (PR #94), His pKa unified 6.0→6.5 (Bjellqvist 1993) across presynth_check.py and physchem.py, METHODS.md safety abs() correction, ensemble.py docstring with config weight references (PR #95), Discovery prediction tracked through PRs #92–#95 (PR #96), WET_LAB_HANDOFF version tag + PROLINE_RICH_INTRACELLULAR QC flag table row + amphipathic_score/charge_ph74 score reference rows (PR #97), EXPERT_REVIEW_PACK new CSV columns note (PR #98), 12 new CLI tests covering generate-batch, batch-pack, pilot-panel success path, batch-pack markdown, redundancy + optimal-cluster-rep sections, novelty error paths, family structural warnings — 1304 tests, 99% coverage; ROADMAP extended through PRs #93–#98 (PR #99)
 
 ---
 
@@ -14,7 +14,7 @@ panel nominated by the computational pipeline. It covers the likelihood of wet-l
 each stage, identifies the key risk factors in the current nominee set, and lists concrete
 improvements already implemented or recommended.
 
-**Bottom line (post-PR #95, 7 scaffold families, AUROC 0.8420):** The pilot panel has a
+**Bottom line (post-PR #99, 7 scaffold families, AUROC 0.8420):** The pilot panel has a
 ~99.95% probability of yielding ≥1 candidate with MIC ≤ 16 µg/mL (P(zero active) = 0.000508
 across 7 families; per-family breakdown in [`docs/WET_LAB_PROBABILITY.md`](WET_LAB_PROBABILITY.md))
 and **~10–20%** probability of generating "breaking news" publication material (up from 5–12%

diff --git a/docs/ROADMAP.md b/docs/ROADMAP.md
@@ -79,6 +79,12 @@ Implemented during the pre-wet-lab improvement loop (PRs #31–#54):
 - `PROLINE_RICH_INTRACELLULAR` flag in presynth QC — RPMI-1640 parallel assay recommendation for ≥25% Pro; all 4 SEED-009 pilot variants flagged (Krizsan et al. 2014 Angew Chem Int Ed 53:12236) (PR #90)
 - `amphipathic_score` + `charge_ph74` added to pilot panel CSV for wet-lab within-family prioritization (PR #91)
 - Doc sync: Krizsan citation corrected (53:14546 → 53:12236) across ASSAY_PREREGISTRATION + EXPERT_REVIEW_PACK; `make help` target added (PR #92)
+- ROADMAP v0.7.x section added documenting all PRs #73–#92 (PR #93)
+- Test coverage: 5 new tests covering LONG_PEPTIDE flag, no-flags checklist, and length-filter failure mode (PR #94); 12 new CLI tests for generate-batch, batch-pack, pilot-panel success, batch-pack markdown, redundancy + optimal-cluster-rep sections, novelty error paths, family structural warnings — 1304 tests, 99% coverage (PR #99)
+- His pKa unified 6.0 → 6.5 (Bjellqvist 1993) across presynth_check.py and physchem.py; METHODS.md abs() correction; ensemble.py weight docstring (PR #95)
+- Discovery prediction tracked through PRs #92–#95 in DISCOVERY_PREDICTION.md (PR #96)
+- WET_LAB_HANDOFF.md: version tag corrected, PROLINE_RICH_INTRACELLULAR QC flag table row, `amphipathic_score`/`charge_ph74` score reference table rows added (PR #97)
+- EXPERT_REVIEW_PACK.md: note added on new CSV columns for within-family prioritization (PR #98)
 
 ## v1.0 — Validated dry-lab-to-wet-lab loop