Molecular Structure
Quantization

A machine-readable quantum molecular ontology. Every drug, virus, protein, G-quadruplex, and biosensor signature mapped to a theta triplet on the NEMP sphere. RDF/Turtle. SPARQL-queryable. Open for academic partnership.

Download msq.ttl View on GitHub

Theta Encoding

Every entity in the knowledge graph receives a theta triplet computed via Non-Euclidean Molecular Partitioning (NEMP). The encoding maps different physical properties to each axis depending on entity type.

Entity Type	theta_RX	theta_RY	theta_RZ
`msq:Compound`	LogP	TPSA	Molecular Weight
`msq:Virus`	G4 density / 1000 nt	GC content	Genome length
`msq:Protein`	GRAVY hydrophobicity	Isoelectric point	Sequence length
`msq:GQuadruplex`	G-island length	Loop length	Tm stability
`msq:BiosensorSignature`	334 nm peak	445 nm excimer	334/445 ratio

Entity Classes

msq:Compound

Approved drugs, failed drugs, investigational, orphan-designated, G4 stabilizers/destabilizers, Hsp modulators, Cx43 modulators, antivirals, cosmetic actives, environmental contaminants, immunomodulators.

msq:Virus

Baltimore-classified viral species. Pandemic-capable vs. geographically contained (Cx43 gap junction framework). Zoonotic spillover tracking. NCBI Taxonomy linked.

msq:Protein

Viral proteins (spike, RdRp, protease, neuraminidase, capsid) and host proteins (Cx43, Hsp70/90, Grp78, viperin, interferons, interleukins). UniProt linked.

msq:GQuadruplex

G4 structures in viral genomes (PQS per Lavezzo et al. 2018) and host genomes. Topology, conservation score, genomic location, strand polarity, Tm stability.

msq:BiosensorSignature

Expected G4 quantum fluorescence profile for radioptic detection. 334 nm intrinsic emission, 445 nm excimer, KCl stability control. Patent-protected technology.

msq:OrphanDrug

Rare disease compounds. Theta read-across from approved drugs enables safety profiling when patient populations are too small. Linked to Orphanet (ORDO) and MONDO.

Namespaces

msq: Ontology vocabulary — classes, properties, relationships

msqc: Compound instances (by SMILES hash or name)

msqv: Virus instances (by NCBI taxon ID)

msqp: Protein instances (by UniProt accession)

msqg4: G-quadruplex instances (by PQS sequence + virus)

msqi: Interaction instances (edges in the knowledge graph)

msqbio: Biosensor signature instances

msqorph: Orphan drug / rare disease linkages

Example: Aspirin

@prefix msq:  <https://msq.mosaeq.com/ontology/> .
@prefix msqc: <https://msq.mosaeq.com/compound/> .

msqc:aspirin
    a msq:DrugApproved ;
    msq:smiles          "CC(=O)OC1=CC=CC=C1C(=O)O" ;
    msq:theta_RX        "1.948"^^xsd:decimal ;
    msq:theta_RY        "4.296"^^xsd:decimal ;
    msq:theta_RZ        "1.607"^^xsd:decimal ;
    msq:molecularWeight "180.16"^^xsd:decimal ;
    msq:qubits          "8"^^xsd:integer ;
    msq:totalGates      "46"^^xsd:integer ;
    msq:computedBy      <https://mosaeq.com> ;
    # First entity in the theta registry — 23 March 2026

Interoperability

The msq ontology links to established biomedical vocabularies: ChEBI (compounds), UniProt (proteins), NCBI Taxonomy (viruses), Orphanet/ORDO (rare diseases), MONDO (disease ontology), and DrugBank. Any SPARQL endpoint can import and federate queries across the knowledge graph.

Content-negotiation: request text/turtle from any entity URI to receive its RDF representation. Request text/html for the human-readable view.

Academic Partnership

We are actively seeking research partnerships with universities and hospitals working on G-quadruplex biology, antiviral drug discovery, rare disease therapeutics, and quantum biosensor development. The ontology is version-controlled on GitHub and open to collaborative extension.

Contact: partnerships@mosaeq.com

References

Lavezzo E, Berselli M, Frasson I, Perrone R, Palu G, Brazzale AR, Richter SN, Toppo S. G-quadruplex forming sequences in the genome of all known human viruses: A comprehensive guide. PLoS Comput Biol 14(12): e1006675 (2018).

Balanikas E, Gustavsson T, Markovitsi D. Fluorescence of bimolecular guanine quadruplexes: from femtoseconds to nanoseconds. J Phys Chem B 127(1): 172-179 (2023).

Ruggiero E, Richter SN. G-quadruplexes and G-quadruplex ligands: targets and tools in antiviral therapy. Nucleic Acids Res (2018).

Shajari E et al. G-quadruplex aptamer-based colorimetric biosensor for HPV18 detection. Microchemical J 221: 116811 (2026).

Molecular StructureQuantization