{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T11:41:42Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 21.8, "error": "Reading additional input from stdin...\nOpenAI Codex v0.153.4\n--------\nworkdir: R:\\02_PROJECTS\\02_Meta_Models_Platforms\\Ver.cy\\current\\thing-registry-backlog\nmodel: gpt-6-astra\nprovider: openai\napproval: never\nsandbox: read-only\nreasoning effort: none\nreasoning summaries: none\nsession id: 01a0956b-5de2-7681-b86a-7283826d0569\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: nucleic acid tertiary structure\nSense to describe: (none recorded)\nDomain code: PHY.OBJ\nAlso known as: (none)\n\n\nContext for this batch of 1001 things:\n#", "usd": 0.0, "recall": true }, "codex": { "seconds": 65.4, "error": "Reading additional input from stdin...\nOpenAI Codex v0.153.4\n--------\nworkdir: R:\\02_PROJECTS\\02_Meta_Models_Platforms\\Ver.cy\\current\\thing-registry-backlog\nmodel: gpt-6-astra\nprovider: openai\napproval: never\nsandbox: read-only\nreasoning effort: none\nreasoning summaries: none\nsession id: 01a0956b-5dec-7002-994c-d7776f6861a4\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: nucleic acid tertiary structure\nRegistry id: vr.tr.nucleic-acid-tertiary-structure\nPlane / domain: PHY / PHY.OBJ\nRegistry definition: (none recorded)" } }, "enrichment": { "pass": 3, "engine": "claude", "producedAt": "2026-10-06T12:00:00Z", "ingestedAt": "2026-10-06T08:55:40+00:00", "fields": [ "agent_conduct", "ethics", "failure_modes_and_hazards", "owners", "visual_identification" ] }, "gate": { "passed": true, "version": "1.0", "at": "2026-10-07T10:10:30+00:00", "evidence": [ "completeness 1.00", "sense: Wikidata description", "2 live sources", "review by codex: pass" ] } }, "metaModel": { "id": "THING-Q3823894", "registryId": "vr.tr.nucleic-acid-tertiary-structure", "name": "nucleic acid tertiary structure", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.OBJ" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q3823894/", "model": { "registry_id": "vr.tr.nucleic-acid-tertiary-structure", "name": "nucleic acid tertiary structure", "purpose": "Enable an AI agent to identify a nucleic acid's three-dimensional fold, assess evidence for its conformational state, and judge which comparisons or interventions that evidence supports.", "definition": "Nucleic acid tertiary structure is the three-dimensional organization of a DNA or RNA molecule, including the spatial arrangement and interactions of its secondary-structure elements.", "scope_statement": "This model owns the three-dimensional organization and conformational ensemble of DNA, RNA, or mixed nucleic acid assemblies under specified conditions, including spatial contacts, topology, stabilization, and structural uncertainty; it treats tertiary structure as a physical organization of molecules rather than as their sequence or a coordinate file.", "in_scope": [ "Three-dimensional arrangement of nucleic acid helices, loops, junctions, and other structural elements", "Spatial contacts and interactions that organize a fold", "Strand connectivity, assembly boundaries, and topology relevant to the fold", "Conformational ensembles, transitions, and dependence on environmental conditions", "Experimental or computational evidence, structural coverage, and uncertainty" ], "out_of_scope": [ "Nucleotide sequence identity and chemical composition except where needed to map or explain a fold", "Secondary-structure descriptions considered independently of three-dimensional organization", "Protein folds and complete nucleoprotein assemblies beyond their effects on the nucleic acid conformation", "General nucleic acid synthesis, degradation, and metabolism", "Coordinate-file formats, repository operations, and software implementation", "Whole-chromosome organization except where explicitly included in the modeled structural unit" ], "distinguishing_features": [ "A sequence or base-pairing diagram alone does not identify the tertiary structure: spatial organization or evidence constraining it must also be recorded.", "The same nucleotide sequence may have multiple conformations, so sequence identity is insufficient to establish structural identity.", "A coordinate model represents a proposed or measured conformation; its existence does not establish that every modeled contact occurs under the conditions of interest.", "Protein or ligand binding belongs here through its effect on nucleic acid geometry; the complete partner structure belongs to a neighboring model.", "Descriptions of DNA supercoiling or chromosome packing require an explicit structural boundary because tertiary structure and higher-order organization can overlap in usage." ], "characteristics": [ { "name": "Nucleic acid composition", "kind": "category", "unit_or_values": "DNA; RNA; mixed DNA-RNA; chemically modified nucleic acid", "why_it_matters": "Identifies which backbone and residue chemistries must be considered when interpreting geometry and interactions." }, { "name": "Structural unit", "kind": "relation", "unit_or_values": "Referenced molecules, strand identifiers, residue ranges, and assembly stoichiometry", "why_it_matters": "Establishes exactly which molecular material the fold describes." }, { "name": "Connectivity and topology", "kind": "category", "unit_or_values": "Linear or circular strands; strand breaks; documented knot, linking, or supercoiling descriptors where applicable", "why_it_matters": "Separates arrangements that look locally similar but differ in connectivity or global constraints." }, { "name": "Tertiary contact network", "kind": "relation", "unit_or_values": "Residue- or atom-indexed contacts with interaction type, geometric criterion, and evidence", "why_it_matters": "Records which interactions support the proposed spatial organization." }, { "name": "Global and local geometry", "kind": "measurement", "unit_or_values": "Distances and radius of gyration in Å or nm; angles in degrees; each with a defined atom selection", "why_it_matters": "Makes compactness, inter-element orientation, and structural comparisons reproducible." }, { "name": "Conformational state", "kind": "state", "unit_or_values": "Defined state identifier; single modeled conformation or ensemble; population estimates when supported", "why_it_matters": "Prevents one structural snapshot from being treated as the only accessible fold." }, { "name": "Environmental conditions", "kind": "measurement", "unit_or_values": "Temperature in K or °C; pH; ion and ligand identities with concentrations in mol/L; applied force in pN when relevant", "why_it_matters": "Conditions establish the context in which a conformation was observed or predicted." }, { "name": "Structural evidence and confidence", "kind": "relation", "unit_or_values": "Source-linked observations, methods, residue coverage, validation metrics, and method-specific confidence measures", "why_it_matters": "Determines which structural claims can support recognition, comparison, or intervention." } ], "affordances": [ "Map observed or predicted spatial features to a defined nucleic acid construct.", "Compare folds using explicit residue correspondence, structural coverage, and compatible conditions.", "Locate candidate tertiary contacts and identify observations needed to test them.", "Distinguish supported conformational changes from differences attributable to construct, method, or environment.", "Propose mutations, ion changes, or binding perturbations to test a structural hypothesis.", "Assess whether a structure is sufficiently supported for a specified downstream use." ], "agent_conduct": { "may": [ "Describe the tertiary structure of a DNA or RNA molecule from experimental or predicted data, naming the source.", "State the method and resolution behind a structure." ], "must_not": [ "Present a predicted structure as experimentally determined.", "Overstate the confidence of a structure model in reports.", "Use structural data to suggest unproven medical treatments.", "Submit structures to public databases without proper validation." ], "requires_human": [ "Publishing or depositing a new structure.", "Using a structure to guide drug design decisions." ] }, "ethics": { "considerations": [ "Wrong structures in public databases mislead many later studies.", "Overstated claims can raise false hope in patients." ], "affected_parties": [ "Researchers", "Patients awaiting treatments", "Database users" ] }, "owners": { "steward": "The research group that determined it; structure databases hold the public record.", "master_systems": [ "Protein Data Bank and nucleic acid structure databases" ] }, "visual_identification": [ "Seen only through experimental data, such as diffraction maps, cryo-electron microscopy or NMR.", "Shown as three-dimensional models of folded helices, loops and junctions." ], "failure_modes_and_hazards": [ "Errors in models from poor data or over-fitting.", "Misinterpretation of predicted structures as facts." ], "what_it_is_for": [ "Nucleic acid tertiary structure is studied in structural biology to explain how DNA and RNA folding supports molecular recognition, catalysis and regulation.", "Three-dimensional models are used to compare conformations, interpret experiments and evaluate proposed interactions with proteins or other molecules.", "Any interpretation depends on the experimental conditions and the uncertainty of the structural evidence." ], "standards_and_regulation": [ "The PDBx/mmCIF data standard, maintained by the Worldwide Protein Data Bank, specifies how deposited nucleic acid structures and their associated structural metadata are represented." ] }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q3823894: nucleic acid tertiary structure", "url": "https://www.wikidata.org/wiki/Q3823894", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: Nucleic acid tertiary structure", "url": "https://en.wikipedia.org/wiki/Nucleic_acid_tertiary_structure", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "structural-unit-and-topology", "name": "Structural unit and topology", "description": "Defines the molecular extent, connectivity, and organizational scale of the tertiary structure.", "rationale": "A fold cannot be interpreted reliably without knowing which residues and strands it includes and which topological constraints apply.", "layers": [ { "id": "construct-and-residue-mapping", "name": "Construct and residue mapping", "description": "Connects the structural description to the actual nucleic acid material.", "findings": [ { "id": "molecular-extent", "name": "Molecular extent", "description": "Record strand identities, residue ranges, modifications, and differences between the studied construct and its reference molecule.", "questions": [ { "text": "Which DNA, RNA, or mixed strands and residue ranges constitute the structural unit?", "kind": "boundary", "id": "molecular-extent-q01" }, { "text": "Which source establishes the construct sequence, modifications, strand breaks, and residue numbering?", "kind": "provenance", "id": "molecular-extent-q02" } ] } ] }, { "id": "connectivity-and-organizational-scale", "name": "Connectivity and organizational scale", "description": "Separates local folding, multistrand assembly, and larger-scale organization.", "findings": [ { "id": "topological-boundary", "name": "Topological boundary", "description": "Record strand connectivity and justify whether linking, supercoiling, or intermolecular organization belongs within this structural unit.", "questions": [ { "text": "Are the strands linear, circular, nicked, or otherwise connected, and what evidence establishes that connectivity?", "kind": "definition", "id": "topological-boundary-q01" }, { "text": "Which intermolecular contacts or topological features belong to this fold, and which belong to a larger assembly?", "kind": "boundary", "id": "topological-boundary-q02" } ] } ] } ] }, { "id": "fold-architecture-and-contacts", "name": "Fold architecture and contacts", "description": "Describes the spatial organization that goes beyond a sequence or secondary-structure map.", "rationale": "Recognition and comparison require explicit geometry and contacts rather than a fold label alone.", "layers": [ { "id": "three-dimensional-element-arrangement", "name": "Three-dimensional element arrangement", "description": "Positions helices, loops, junctions, and other elements relative to one another.", "findings": [ { "id": "spatial-architecture", "name": "Spatial architecture", "description": "Record structural elements and the measurements or constraints establishing their relative placement.", "questions": [ { "text": "Which helices, loops, junctions, or other elements define the fold, and how are they mapped to residues?", "kind": "definition", "id": "spatial-architecture-q01" }, { "text": "Which distances, orientations, or compactness measurements distinguish the proposed arrangement from plausible alternatives?", "kind": "measurement", "id": "spatial-architecture-q02" } ] } ] }, { "id": "tertiary-interaction-network", "name": "Tertiary interaction network", "description": "Captures contacts that connect structural elements and organize the three-dimensional fold.", "findings": [ { "id": "contact-assignment", "name": "Contact assignment", "description": "Record candidate base interactions, stacking, backbone contacts, and other tertiary contacts with explicit assignment criteria.", "questions": [ { "text": "Which residue pairs or groups form proposed tertiary contacts, and what geometric or experimental criteria identify each contact?", "kind": "measurement", "id": "contact-assignment-q01" }, { "text": "Which contacts are directly supported, inferred from a structural model, or proposed by analogy?", "kind": "provenance", "id": "contact-assignment-q02" } ] } ] } ] }, { "id": "stabilization-and-conformational-change", "name": "Stabilization and conformational change", "description": "Relates fold states to solution conditions, binding partners, and perturbations.", "rationale": "A tertiary structure is condition-dependent, and a usable model must distinguish a static representation from supported conformational behavior.", "layers": [ { "id": "environment-and-binding", "name": "Environment and binding", "description": "Records the conditions and associated molecules relevant to the observed conformation.", "findings": [ { "id": "condition-dependent-fold", "name": "Condition-dependent fold", "description": "Associate each structural state with measured conditions and evidence for ion, ligand, or protein effects.", "questions": [ { "text": "Under what temperature, pH, ionic composition, concentration, and binding conditions was this state characterized?", "kind": "measurement", "id": "condition-dependent-fold-q01" }, { "text": "What evidence distinguishes a specifically bound ion or ligand from a general solution effect or an uncertain assignment?", "kind": "provenance", "id": "condition-dependent-fold-q02" } ] } ] }, { "id": "ensembles-and-transitions", "name": "Ensembles and transitions", "description": "Distinguishes alternative conformations, their populations, and supported transitions.", "findings": [ { "id": "state-populations-and-exchange", "name": "State populations and exchange", "description": "Record alternative states and distinguish measured heterogeneity from uncertainty in structural reconstruction.", "questions": [ { "text": "Which alternative conformations are supported, and are their populations or exchange times measured under comparable conditions?", "kind": "measurement", "id": "state-populations-and-exchange-q01" }, { "text": "Does the reported ensemble represent physical conformational variation, uncertainty in inference, or a mixture of both?", "kind": "boundary", "id": "state-populations-and-exchange-q02" }, { "text": "Which controlled perturbation could test a proposed transition or stabilizing interaction?", "kind": "action", "id": "state-populations-and-exchange-q03" } ] } ] } ] }, { "id": "structural-evidence-and-permitted-inference", "name": "Structural evidence and permitted inference", "description": "Connects structural claims to observations, validation, and the decisions they can support.", "rationale": "Incomplete coverage, method limitations, and prediction uncertainty can change whether a proposed fold is useful for a particular task.", "layers": [ { "id": "evidence-coverage-and-validation", "name": "Evidence coverage and validation", "description": "Tracks where the structure is constrained and where interpretation remains uncertain.", "findings": [ { "id": "claim-level-structural-support", "name": "Claim-level structural support", "description": "Link structural assertions to experimental observations or computational predictions and record unresolved regions and validation concerns.", "questions": [ { "text": "Which accessible sources and underlying observations support each major architectural or contact claim?", "kind": "provenance", "id": "claim-level-structural-support-q01" }, { "text": "Which residues, interactions, or relative domain positions are unresolved, weakly constrained, or affected by validation concerns?", "kind": "measurement", "id": "claim-level-structural-support-q02" }, { "text": "Which reported metrics assess experimental fit, stereochemical plausibility, or prediction confidence, and what does each metric actually establish?", "kind": "definition", "id": "claim-level-structural-support-q03" } ] } ] }, { "id": "comparison-and-intervention-readiness", "name": "Comparison and intervention readiness", "description": "Sets the evidential requirements for comparing folds or acting on structural hypotheses.", "findings": [ { "id": "supported-structural-use", "name": "Supported structural use", "description": "Record the intended use, comparable structural regions, and unresolved assumptions that could affect a decision.", "questions": [ { "text": "Which residue correspondence, atom selection, alignment procedure, and condition differences must be specified before comparing two structures?", "kind": "boundary", "id": "supported-structural-use-q01" }, { "text": "Is the available evidence adequate for the proposed use, such as fold classification, mutation design, or binding-site investigation?", "kind": "action", "id": "supported-structural-use-q02" }, { "text": "What additional observation would most directly resolve the uncertainty limiting that use?", "kind": "action", "id": "supported-structural-use-q03" } ] } ] } ] }, { "id": "evidence-and-external-alignment", "name": "Evidence and external alignment", "description": "What the world already says about this thing, gathered so the model can be checked against it.", "rationale": "A model that cannot be lined up against existing standards, identifiers and practice cannot be adopted by anyone who already uses them.", "layers": [ { "id": "reported-evidence", "name": "Reported evidence", "description": "Findings from the breadth pass, kept separate from the structural claims.", "findings": [ { "id": "evidence-confidence-notes", "name": "Check these first", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "The listed kinds are overlapping architectural classes, not an exhaustive or mutually exclusive taxonomy.", "Classification of pseudoknots, triplexes and quadruplexes as secondary, tertiary or quaternary structure varies with convention and the number of participating molecules.", "There is no useful universal measurement range: dimensions, stability and conformational dynamics depend on sequence, molecular length, binding partners and solution conditions." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of nucleic acid tertiary structure this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-kinds", "name": "Kinds and varieties", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "Compact globular RNA folds", "RNA pseudoknot architectures", "DNA supercoiled conformations", "Nucleic acid triple-helical architectures", "G-quadruplex architectures" ], "questions": [ { "id": "evidence-kinds-q01", "text": "Which of these kinds and varieties hold for the sense of nucleic acid tertiary structure this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-identifiers", "name": "Identifiers and schemes", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ { "scheme": "Protein Data Bank (PDB) accession", "value_or_pattern": "An accession identifying a deposited three-dimensional structure", "note": "Identifies an individual structural entry, which may contain DNA, RNA or nucleic acid-protein complexes; it does not identify tertiary structure as a general concept." } ], "questions": [ { "id": "evidence-identifiers-q01", "text": "Which of these identifiers and schemes hold for the sense of nucleic acid tertiary structure this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-real-world-use", "name": "Real-world use", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "Explaining how ribozymes position functional groups for catalysis", "Understanding tRNA folding and recognition during translation", "Studying how DNA supercoiling affects replication and transcription", "Designing RNA aptamers and nucleic acid nanostructures", "Identifying structured RNA sites for molecular recognition and drug discovery" ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of nucleic acid tertiary structure this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-failure-modes-and-hazards", "name": "Failure modes and hazards", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "Misfolding or kinetic trapping can prevent an RNA molecule from reaching a functional conformation.", "Changes in temperature, pH or ionic conditions can destabilize tertiary contacts.", "Sequence changes can disrupt long-range interactions and alter biological function.", "Alternative DNA structures can impede replication or transcription in some sequence and cellular contexts.", "A single experimentally determined structure may conceal conformational heterogeneity or dependence on experimental conditions." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of nucleic acid tertiary structure this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-neighbours", "name": "Neighbouring kinds and how to tell them apart", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ { "name": "Nucleic acid primary structure", "difference": "Primary structure specifies nucleotide sequence and covalent connectivity; tertiary structure specifies spatial organization." }, { "name": "Nucleic acid secondary structure", "difference": "Secondary structure describes pairing patterns and elements such as stems and loops; tertiary structure describes their three-dimensional arrangement and additional contacts." }, { "name": "Nucleic acid quaternary structure", "difference": "Quaternary structure concerns assembly between separate molecular subunits, although terminology overlaps for multistranded nucleic acid structures." }, { "name": "Chromatin structure", "difference": "Chromatin structure includes DNA packaging with histones and other associated components, extending beyond the conformation of the nucleic acid itself." }, { "name": "Nucleic acid topology", "difference": "Topology concerns properties such as linking and knotting under specified strand constraints; tertiary structure also includes geometric features that can change without altering topology." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of nucleic acid tertiary structure this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Does an existing Vercy world model already own this concept, requiring this registry entry to link to it instead of receiving a separate publication?", "What authoritative definition should delimit tertiary structure across DNA, RNA, multistrand folds, and higher-order nucleic acid organization?", "Which conventions should distinguish tertiary contacts from secondary-structure interactions in cases such as pseudoknots and extended noncanonical pairing?", "Which method-specific evidence and validation criteria are sufficient for each intended downstream use without treating unlike confidence metrics as interchangeable?", "How should structural states be identified across different constructs and conditions when the evidence does not establish whether they are distinct folds or variations within one ensemble?" ], "statistics": { "bundles": 5, "layers": 9, "findings": 14, "questions": 25 } }