OMNIKERNEL-A Evaluator (NO-SIM) v5: Geometry-Only van der Waals Overlap Auditor for Protein Structures

Protein structure assessment is commonly conflated with predictive modeling or simulation-based approaches. This work presents OMNIKERNEL-A Evaluator (NO-SIM) v5, a geometry-only, non-simulative software tool designed to audit the material consistency of existing protein structures. The evaluator computes structural coherence (Σ) from Cα–Cα contact topology and material friction (φ) from van der Waals (VdW) atomic overlap, using only static coordinates from real PDB files (ATOM and optional HETATM records). No molecular dynamics, force fields, statistical training, or synthetic data are employed. A balance criterion of the form Q·Σ > φ is evaluated to identify structures whose geometric coherence is exceeded by steric interpenetration, while an optional entropy veto (ΔS) is applied only when comparing conmensurable structural states of the same protein. OMNIKERNEL-A does not predict protein folding. Instead, it provides an auditable, reproducible framework for identifying steric stress, geometric tension, and structural inconsistency in experimentally resolved models, complementing existing validation pipelines with a strictly non-simulative perspective.