Chiral Boundary Mode Reader: Detecting Instability Zones in Protein Structures
A geometric diagnostic layer that reveals folding‑transition boundaries where prediction systems fail.
Protein folding failures occur not in stable basins but at the boundaries between them — hinge zones, disorder transitions, interface instabilities, and metastable pockets. Existing prediction systems such as AlphaFold excel at stable regions but struggle precisely where structural regimes shift.
The Chiral Boundary Mode (CBM) Reader is a post‑prediction diagnostic tool that identifies these instability boundaries. It converts protein structures into residue‑interaction graphs and computes local symmetry, coupling gradients, torsion variance, and contact‑pattern asymmetry to produce a boundary‑instability map.
CBM is safe, publishable, and model‑agnostic. It does not modify prediction systems; it reveals the geometry of instability that prediction systems cannot see. Demonstrations across intrinsically disordered proteins, allosteric switching proteins, and drug‑binding pockets show that boundary geometry is detectable, meaningful, and scientifically valuable.
Index
Index
1. Abstract
Boundary instability as the dominant failure mode in folding systems; CBM as a diagnostic layer.
2. Introduction — Boundary Geometry in Folding Systems
Stable basins vs transition zones; why folding failures cluster at boundaries; AlphaFold’s limitations in boundary‑dominated regimes.
3. Concept — Chiral Boundary Mode (CBM)
Boundary modes as symmetry‑breaking points, phase transitions, instability surfaces; CBM as a detector of structural tipping points.
4. Method — CBM Reader Pipeline
Input: predicted or experimental structure
Graph extraction: residues → nodes; contacts → edges
Local geometry: contact density, torsion variance, symmetry‑break score, coupling gradient
Boundary score: composite instability metric
Output: boundary‑instability map
5. Demonstration Domains
5.1 Intrinsically Disordered Proteins (IDPs)
Disorder‑order transitions, transient helices, metastable pockets.
5.2 Allosteric Switching Proteins
Hinge boundaries, cooperative propagation paths, conformational transition surfaces.
5.3 Drug‑Binding Pockets
Flexible gates, transient cavities, strain zones, allosteric coupling regions.
6. Why CBM Is Safe and Publishable
No proprietary mechanisms; post‑prediction only; geometric and diagnostic; minimal demonstration requirements.
7. Discussion — Boundary Geometry as a General Principle
Boundary behaviour across proteins, turbulence, power grids, contagion, ecological tipping points; CBM as a general instability‑reader.
8. Conclusion
CBM complements structure‑prediction systems by revealing instability geometry rather than stable folds; boundary geometry is detectable and actionable.
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