What question did this study set out to answer?

The aim is to correct previous errors in the CL5D methodology and explore its applications in protein dynamics.

March 25, 2026Open Access

CL5D Applied to Protein Oligomerization: Corrigendum to Paper 6 and Four Propositions Beyond AlphaFold pLDDT

Key Points

The aim is to correct previous errors in the CL5D methodology and explore its applications in protein dynamics.
Provided a corrigendum for Paper 6 addressing errors in precision and comparisons.
Applied the corrected CL5D pipeline to specific protein structures (BACE1 and MAO-B).
Validated four new propositions against PDB experimental data.
Corrected CL5D Cn scores for BACE1 and MAO-B show excellent phase dynamics.
New propositions reveal that CL5D Cn scores offer insights pLDDT cannot.
Propositions include phase transition trajectories and drug binding site readiness.

Abstract

This combined paper presents two contributions to the CL5D Research Series. Paper 6 v2.0 is a formal corrigendum to Paper 6 (doi:10.5281/zenodo.19043350), correcting three errors: (C1) overclaim of "100% precision in silico," (C2) dismissal of biological stochasticity, and (C3) inappropriate comparison with AlphaFold structural accuracy. The corrected CL5D pipeline (At→Ab→Ex→T→Cn) is applied to PDB structures 6EJ2 (BACE1, Alzheimer) and 2V5Z (MAO-B, Parkinson) under the genomics domain protocol (no 50% gate), yielding Cn = 0.017612 and 0.014417 respectively (both Excellent, Phase I). Paper 10 establishes four propositions demonstrating that CL5D Cn scores provide phase-dynamic information that pLDDT cannot: phase transition trajectories (P1), drug binding site readiness (P2), oligomeric state classification (P3), and disordered region functional roles (P4). All propositions are validated against PDB experimental data. Benchmark BS = 0.00002 (fixed).

CL5D Applied to Protein Oligomerization: Corrigendum to Paper 6 and Four Propositions Beyond AlphaFold pLDDT

Key Points

Abstract

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