From Sequence to an Auditable Fold: Smithian Fold Theory V3 Protein Fold Computational Proof — Preliminary Results

Abstract

From Sequence to an Auditable Fold, version 0.9.3, is the first standalone preliminary-results release from the Smithian Fold Theory V3 Protein Fold computational proof programme. It reports a target-free exact representation, complete interaction custody, a six-axis joint physical relation, certified frontier-search scaling and the preserved development-evidence chronology. The largest independently reconstructed exact parent contains 42,173,082 candidates across 11,012 disjoint shards, with 375,014 completed leaves, 41,798,068 certified prunes and 205 retained frontier states. A separately verified high-attraction census evaluates 583 occupations, dominates 573 and retains 10, including eight new nondominated incumbents. Every empirical classification is method-bound: the corrected historical 4APD reconstruction, fresh 4B19 baseline and unseen 8HJC transfer are adverse for the predecessor or partial selectors they tested, not primary tests of the still-incomplete six-axis system. Later recurrence improves 4B19, remains adverse on 8HJC and regresses from the earlier positive narrowed 1JDM transfer. The full chronology and stronger successor work are reported without erasing any original outcome. Active work continues on the remaining exact fixed-geometry attraction bands, global frontier reconciliation, arbitrary-sequence torsion-protonation-solvent recurrence, development and adverse controls, and the frozen 100-target matched AlphaFold campaign. The exact-solver scaling and independent verification support a strong forecast of continued computational closure. Generalised blind AlphaFold parity is the programme's registered empirical prediction and will be decided by the complete matched campaign. When the full investigation and development programme are complete, this record will be updated through Zenodo's versioning system, preserving the preliminary chronology and all favourable, adverse, null and unavailable evidence.