{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-11T23:44:46Z", "providers": [ "Claude" ], "breadth": "written by Claude from model knowledge without web access - no source was read, every claim is a lead to verify", "pass": 2, "wave": 2, "engine": "claude", "enrichment": { "pass": 3, "engine": "claude", "producedAt": "2026-10-05T23:45:00Z", "ingestedAt": "2026-10-05T20:46:46+00:00", "fields": [ "agent_conduct", "ethics", "owners" ] }, "revisions": [ { "at": "2026-10-07T11:26:00+00:00", "engine": "codex", "fields": [ "definition" ], "answering_review": "dd7aa4a4c79954d47192b13cb79ca2e1b918378d2bc0c96ea50573cf527df7d1" } ], "gate": { "passed": true, "version": "1.0", "at": "2026-10-07T12:16:31+00:00", "evidence": [ "completeness 1.00", "sense: Wikidata description", "2 live sources", "review by codex: pass" ] } }, "metaModel": { "id": "THING-Q2252764", "registryId": "vr.tr.dna-binding-protein", "name": "DNA-binding protein", "version": "0.2.0-wave.2", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.MAT" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q2252764/", "model": { "registry_id": "vr.tr.dna-binding-protein", "name": "DNA-binding protein", "purpose": "Let an agent explain DNA-binding proteins and their kinds, describe binding mechanisms and functions, relate them to gene regulation and disease at a general level, and support database lookups.", "definition": "A protein with DNA-binding domains that confer specific or general affinity for single- or double-stranded DNA; binding may be sequence-specific, as in many transcription factors and restriction and modification enzymes, non-sequence-specific, as in histones and polymerases, or directed toward DNA damage or structure, as in many repair proteins; DNA-binding proteins use varied structural motifs and participate in gene expression, replication, repair and recombination and are classified in protein family databases.", "what_it_is_for": "Proteins that interact with DNA.", "affordances": [ "explain kinds and mechanisms", "describe functions", "relate to regulation and disease", "support database lookups" ], "distinguishing_features": [ "DNA binding", "Structural motifs", "Regulatory roles", "Family classification" ], "appearance": "Not visible; molecular structures resolved by crystallography.", "visual_identification": [ "Binds DNA specifically or non-specifically", "Structural binding motifs", "RNA-binding proteins bind RNA instead" ], "physical_properties": [ { "quantity": "Molecular mass", "unit": "kDa", "typical_range": "", "note": "Molecular mass varies among proteins and is determined from sequence composition or measured by mass spectrometry." }, { "quantity": "Hydrodynamic radius", "unit": "nm", "typical_range": "", "note": "Hydrodynamic radius is measured in solution and depends on protein shape, assembly state and experimental conditions." }, { "quantity": "DNA-binding dissociation constant", "unit": "mol/L", "typical_range": "", "note": "The dissociation constant is measured using equilibrium binding assays with a specified DNA substrate and solution conditions." } ], "families_and_kinds": [ "transcription factors", "histones and chromatin proteins", "polymerases and helicases", "restriction and modification enzymes", "repair, recombination and transposase proteins" ], "related_models": [ { "relation": "is a kind of", "target": "nucleic acid binding protein", "why": "category" }, { "relation": "is a kind of", "target": "protein", "why": "category" }, { "relation": "is related to", "target": "gene expression", "why": "regulation" }, { "relation": "is related to", "target": "deoxyribonucleic acid", "why": "binding target" } ], "identifiers": [], "standards_and_regulation": [ "Protein family databases such as Pfam and InterPro", "Structural data standards", "Research ethics for genetic studies" ], "failure_modes_and_hazards": [ "Confusing specific and non-specific binding", "Outdated family classifications", "Agents giving medical advice on mutations" ], "in_scope": [], "out_of_scope": [], "characteristics": [], "agent_conduct": { "may": [ "Explain how DNA-binding proteins work and their families from scientific sources.", "Distinguish sequence-specific from non-specific binding in explanations." ], "must_not": [ "Interpret a person's own mutation in a DNA-binding protein as medical advice.", "Use outdated family classifications without saying so.", "Overstate the predictive power of binding site predictions.", "Assist genetic engineering outside lawful and approved laboratory settings." ], "requires_human": [ "Using results about DNA-binding proteins in diagnosis or treatment." ] }, "ethics": { "considerations": [ "Mutations in these proteins cause diseases whose carriers need careful counselling.", "Tools built from them, such as gene editors, carry large ethical stakes." ], "affected_parties": [ "Patients and carriers", "Research participants", "Researchers" ] }, "owners": { "steward": "Nobody owns the class; protein databases curate the records.", "master_systems": [ "Protein sequence and structure databases" ] } }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q2252764: DNA-binding protein", "url": "https://www.wikidata.org/wiki/Q2252764", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: DNA-binding protein", "url": "https://en.wikipedia.org/wiki/DNA-binding_protein", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "understand", "name": "Understand", "description": "What DNA-binding proteins are.", "rationale": "Biology.", "layers": [ { "id": "kinds", "name": "Kinds", "description": "Kinds and motifs.", "findings": [ { "id": "kinds-finding", "name": "Kinds", "description": "Kinds.", "questions": [ { "text": "What kinds of DNA-binding proteins exist, and which structural motifs let them recognise DNA?", "kind": "definition" }, { "text": "How do specific and non-specific binding differ?", "kind": "definition" } ] } ] }, { "id": "functions", "name": "Functions", "description": "Functions.", "findings": [ { "id": "functions-finding", "name": "Functions", "description": "Functions.", "questions": [ { "text": "How do DNA-binding proteins regulate transcription, replication, repair, recombination and transposition?", "kind": "definition" }, { "text": "Which entry fits a specific family?", "kind": "action" } ] } ] } ] }, { "id": "study", "name": "Study", "description": "Studying binding.", "rationale": "Methods.", "layers": [ { "id": "methods", "name": "Methods", "description": "Experimental methods.", "findings": [ { "id": "methods-finding", "name": "Methods", "description": "Methods.", "questions": [ { "text": "How is DNA binding studied with techniques such as ChIP-seq, footprinting and structural biology?", "kind": "provenance" }, { "text": "How are binding sites predicted?", "kind": "action" } ] } ] }, { "id": "databases", "name": "Databases", "description": "Databases.", "findings": [ { "id": "databases-finding", "name": "Databases", "description": "Databases.", "questions": [ { "text": "Which databases classify DNA-binding protein families and structures?", "kind": "provenance" }, { "text": "How can a protein be looked up?", "kind": "action" } ] } ] } ] }, { "id": "medicine", "name": "Medicine", "description": "Health relevance.", "rationale": "General information.", "layers": [ { "id": "disease", "name": "Disease", "description": "In disease.", "findings": [ { "id": "disease-finding", "name": "Disease", "description": "Disease.", "questions": [ { "text": "How do mutations in DNA-binding proteins relate to cancer and genetic conditions, according to research?", "kind": "provenance" }, { "text": "Is the user asking about their own genetic results, which needs a clinician?", "kind": "boundary" } ] } ] }, { "id": "tools", "name": "Tools", "description": "As tools.", "findings": [ { "id": "tools-finding", "name": "Tools", "description": "Tools.", "questions": [ { "text": "How are DNA-binding proteins used as tools, from restriction enzymes to engineered nucleases?", "kind": "provenance" }, { "text": "Which entry fits genome editing?", "kind": "action" } ] } ] } ] }, { "id": "learn", "name": "Learn", "description": "Teaching and history.", "rationale": "Education.", "layers": [ { "id": "teach", "name": "Teach", "description": "Teaching.", "findings": [ { "id": "teach-finding", "name": "Teach", "description": "Teaching.", "questions": [ { "text": "How can DNA-protein interactions be taught with structures and examples?", "kind": "action" }, { "text": "Which misconceptions arise?", "kind": "provenance" } ] } ] }, { "id": "history", "name": "History", "description": "History.", "findings": [ { "id": "history-finding", "name": "History", "description": "History.", "questions": [ { "text": "How were DNA-binding proteins discovered, from repressors to zinc fingers?", "kind": "provenance" }, { "text": "Which references are standard?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Should transcription factors be a separate entry?", "How should databases be linked?", "How should structures be linked?" ], "statistics": { "bundles": 4, "layers": 8, "findings": 8, "questions": 16 } }