DOI: 10.5281/zenodo.18530013
title: Structural Integrity Index (SII) Reference Database for Biomolecular Quality Assessment.

description: Structural Integrity Index (SII) Reference Database for Biomolecular Quality Assessment

This dataset provides reference Structural Integrity Index (SII) values for 9 representative biomolecular systems, including DNA, RNA, proteins, viral complexes, and pathological conformations.

The SII is a proprietary geometric metric (0-100 scale) developed by Juan Camilo Suarez Sarquez to assess structural coherence and functional viability of complex biomolecular architectures through advanced computational geometric analysis.

Key applications include quality assessment of AI-predicted structures (AlphaFold), drug design screening, gene therapy safety evaluation (CRISPR), bioelectronics development, and early detection of pathological conformations.

The calculation methodology is PROPRIETARY and PATENT-PENDING. For access to the computational tool or collaboration inquiries, contact: Bakthuarq@gmail.com
description: ABOUT THE STRUCTURAL INTEGRITY INDEX (SII):

The SII metric evaluates local structural stress states in three-dimensional molecular space using a multi-step computational framework. Unlike traditional positional metrics (RMSD, TM-Score), the SII provides a standardized assessment of geometric coherence on a 0-100 scale.

DATASET CONTENTS:

This initial release (v1.0) includes SII reference values for 9 structures:- High-integrity systems: CRISPR-Cas9 (99.6), Protein G (99.8), Telomeres (98.7)- Functional RNAs: tRNA (82.1)- Viral proteins: SARS-CoV-2 Spike (78.9)- Pathological states: Prions (76.5), p53 tumor suppressor (71.2)- Reference baseline: B-DNA (50.0)- Damaged structures: Cisplatin-DNA (22.3)

INTERPRETATION GUIDE:

- 95-100: Exceptional structural coherence (molecular precision tools)- 85-94: High integrity (genomic guardians, stable proteins)- 70-84: Moderate stability (functional RNAs, dynamic proteins)- 50-69: Standard biological baseline- 30-49: Structural stress detected- 0-29: Severe degradation or pathological states

APPLICATIONS IN RESEARCH:

1. Structure Validation: Quality control for AlphaFold, RosettaFold, and other AI-predicted structures2. Drug Discovery: Screening structural stability of protein-ligand complexes3. Gene Therapy: Safety assessment of CRISPR systems and off-target risk prediction4. Bioelectronics: Evaluating bio-nano interface compatibility for implants and sensors5. Disease Research: Early detection of misfolding in neurodegenerative diseases

INTELLECTUAL PROPERTY & METHODOLOGY:

The SII calculation methodology, including specific mathematical derivations, internal calibration constants, baseline normalization parameters, and algorithmic implementations, are PROPRIETARY and PATENT-PENDING. These components are maintained as trade secrets to protect authorship and enable commercial applications.

This public dataset contains only the reference SII scores and PDB identifiers. The underlying computational framework is not disclosed.

LICENSING:

- Academic/Non-Commercial Use: Licensed under CC BY-NC 4.0- Commercial Use: Requires separate licensing agreement- Reverse Engineering: Strictly prohibited- AI Training: Integration into proprietary ML models requires authorization

CITATION:

Suarez Sarquez, J.C. (2026). Structural Integrity Index (SII) Reference Database for Biomolecular Quality Assessment. Zenodo. DOI: [assigned upon publication]

ACCESS & COLLABORATION:

For access to the SII calculation tool, commercial licensing, technical documentation (subject to NDA), or collaboration proposals, contact:

Juan Camilo Suarez SarquezEmail: Bakthuarq@gmail.com

The author welcomes inquiries from academic researchers, biotechnology companies, pharmaceutical firms, and AI/ML developers working in structural biology and drug discovery.