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Research-Stack/binding-site
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Allaun Silverfox 35ad40cfae binding-site: 3 outlines, 1,300 lines, Hachimoji × protein structures 
BindingSiteHachimoji.lean (589 lines):
  - 50-token amino acid vocabulary (20 core + 30 modified)
  - 8-state Hachimoji classification for residues
  - Extended Fisher metric on 50-simplex (Chentsov unique)
  - Chaos game basin discovery with Sidon addressing
  - Typed BindingSiteReceipt compatible with PVGS-DQ

BindingSiteEntropy.lean (376 lines):
  - Information entropy per residue site (Void-X Eq. 3)
  - Entropy from B-factors (PDB) or cluster diversity
  - Bindability score B* normalized to 0-100
  - Sidon address generation from entropy profiles
  - Fisher-Rao approximate distance between sites

BindingSiteCodec.lean (335 lines):
  - pdbToReceipt : PDB ID → BindingSiteReceipt (one function)
  - screenDruggable : filter library for bindable pockets
  - rankByEnergy : sort by dual quaternion energy
  - Test cases: EGFR (1YY9), Tautomerase (9MUA), KIR2DL1 (9HML)

Architecture: PDB → entropy profile → Hachimoji state → PVGS params
  → dual quaternion energy → typed receipt → PVGS-DQ system

All three files compile as outlines with sorry for future proofs.
2026-06-21 04:16:34 -05:00
..
BindingSiteCodec.lean binding-site: 3 outlines, 1,300 lines, Hachimoji × protein structures 2026-06-21 04:16:34 -05:00
BindingSiteEntropy.lean binding-site: 3 outlines, 1,300 lines, Hachimoji × protein structures 2026-06-21 04:16:34 -05:00
BindingSiteHachimoji.lean binding-site: 3 outlines, 1,300 lines, Hachimoji × protein structures 2026-06-21 04:16:34 -05:00