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feat: add SEED-007 (Bombolitin II) + SEED-008 (Puroindoline-a) for novel scaffold diversity (#42) - #41
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…vel scaffold diversity - SEED-007: IKITTMLKKLG from Bombus terrestris bumblebee venom (Argiolas & Pisano 1985); novelty=0.615, serum_stability=0.636; amphipathic helix mechanism distinct from SEED-006 - SEED-008: FPVTWRWWKWWKG puroindoline-a Trp domain from Triticum aestivum (Dubreil et al. 1997); novelty=0.667 (highest of all 8 seeds); Trp-mediated lipid bilayer disruption - Pool regenerated: 461 → 583 entries (8 seeds × ~73 variants each)
cschanhniem
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Jun 28, 2026
…th QC (#41) (#42) * feat: add N-terminal acetylation flag and D-amino Wave 2 guidance to presynth QC - SynthQC gains n_acetylation_recommended/n_acetylation_reason fields: when interior trypsin sites exist, flag recommends Nα-Ac at zero synthesis cost to block aminopeptidase entry (Creighton 1993; Dhankhar et al. 2023) - SynthQC gains wave2_d_substitutions list: up to 3 most-N-terminal interior K/R sites yield D-Lys/D-Arg substitution guidance for Wave 2 synthesis (expected t½ gain 3–10×; Wade et al. 1990 PNAS) - Both guidance flags appended AFTER synthesis_difficulty is computed (zero synthesis cost — must not inflate difficulty rating) - to_dict() exposes all three new fields - WET_LAB_HANDOFF.md: two new rows in the QC flags table - 10 new tests in TestWave2Guidance; full 954-test suite green * test: add missing edge-case coverage for Wave 2 guidance (C-terminal K/R, 1-indexed positions, empty seq) - HIGH: lock in that a C-terminal-only K/R does NOT trigger N-acetylation flags (regression guard) - MEDIUM: assert 1-indexed position strings in wave2_d_substitutions for RRWQWRMKKLG - MEDIUM: empty-sequence smoke test (parallel to TestCTerminalAmidation) - LOW: fix misleading comment in interior-trypsin-sites test - LOW: assert n_acetylation_reason is non-empty and contains "acetylat"
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Summary
SEED-007: Bombolitin II (IKITTMLKKLG) from Bombus terrestris bumblebee venom
SEED-008: Puroindoline-a Trp domain (FPVTWRWWKWWKG) from Triticum aestivum wheat endosperm
Pool regenerated: ~461 → 583 entries (8 seeds × ~73 variants each)
Impact on Discovery Probability
Test plan