Junior B.
75f5383961
§12.3-12.4 first binding result on ARM Mac. - Toolchain SOLVED: AutoDock Vina 1.2.5 mac binary (Rosetta) + open-babel (brew). No conda, no MLX. dock_positive_controls.py runs end-to-end. - Cross-dock known binders + negatives into Hb (5E83) and PKR (8XFD), box centered on co-crystal ligands (5L7=voxelotor, WV2=mitapivat). Finding: raw Vina affinity ranks almost perfectly by MOLECULAR SIZE (mitapivat > voxelotor > decitabine/caffeine > hydroxyurea) in both pockets — mitapivat wins even on hemoglobin it doesn't target. Raw score can't distinguish target-specific binding: the docking analog of the connectivity specificity problem. Next: redocking-RMSD validation + ligand-efficiency normalization. Note: machine is 24GB (not 96GB per PLAN §2), capping local AF3-class inference. tools/ gitignored (vina binary). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
37 lines
577 B
Plaintext
37 lines
577 B
Plaintext
# Data — never commit raw or processed data; keep directory structure via .gitkeep.
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# Re-include directories first (!data/**/), else .gitkeep inside an excluded dir
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# cannot be un-ignored.
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data/raw/**
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data/processed/**
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data/results/**
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!data/**/
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!data/**/.gitkeep
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# Python
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__pycache__/
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*.py[cod]
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*.egg-info/
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.eggs/
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build/
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dist/
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.venv/
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venv/
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env/
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# Jupyter
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.ipynb_checkpoints/
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*/.ipynb_checkpoints/
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# Tooling caches
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.pytest_cache/
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.ruff_cache/
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.mypy_cache/
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# OS / editor
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.DS_Store
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.idea/
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.vscode/
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# Local tool binaries (refetch per docs/structure_binding_notes.md)
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tools/
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