[SUPERSEDED-09-26-2026 consolidated into zenodo.22993176] Structural Mapping of Amyloidogenic and Neurodegenerative Disease Targets -- Neuro Research Dataset
Description
Dataset Title: Structural Mapping of Amyloidogenic and Neurodegenerative Disease Targets -- Neuro Research Dataset v1.1
Overview: Focuses on protein misfolding, nucleation, and aggregation pathways in ALS, Alzheimer's, and Parkinson's disease (e.g., HTT, SNCA, LRRK2, APOE4, APP, SOD1). Mapped coordinate structures show expanded ligand cavities to design small-molecule stabilizers that lock the monomeric state and prevent toxic oligomerization.
Computational Methodology: Target structures are optimized using the NRC CASP-17 Pure Math Folding Engine. This pipeline applies C-alpha harmonic guide potential constraints ($k_{guide} = 0.5$) for comparative modeling (or $k_{guide} = 0.0$ for ab-initio modeling), followed by sidechain relaxation and pocket expansion simulations to identify allosteric and active cavities. All coordinates are audited using the Trageser Tensor Theorem (TTT-7) lattice-parity verification to eliminate steric clashes (minimum inter-atomic distance > 1.10 Å) and loop hallucinations.
License: Distributed under Creative Commons Attribution 4.0 International (CC BY 4.0) to enable open, commercial, and academic therapeutic drug design.
Principal Investigator: James Paul Trageser
Affiliation: Nexus Resonance Codex
ORCID: 0009-0006-6678-2908
X (Twitter): @jtrag
Repository: https://GitHub.com/Nexus-Resonance-Codex/Drug-Discovery