uniprot-search

name	uniprot-search
description	Search UniProtKB for proteins by name, gene, organism, or keyword and retrieve accessions plus functional annotation. Use when the user wants protein metadata, function, sequence, or identifier mapping. Uses the plugin's built-in read-only UniProt MCP tool for discovery — no credential or install needed.
license	Apache-2.0

UniProt Protein Search (Codex-native)

Codex-native protein search wired to this plugin's built-in read-only MCP tool. Inspired by Google DeepMind's uniprot-database (science-skills, Apache-2.0); the MCP integration is Codex Science's own.

How to run

1. Search with the plugin MCP tool science_search_uniprot:
   • arguments: query (protein/gene/organism/keyword, ≤500 chars; UniProt query syntax like gene:TP53 AND organism_id:9606 works), limit (1–10, default 5).
   • returns a JSON list of {id, title, url} — id is the primary accession, title the recommended protein name, url the entry page.
2. Disambiguate: if several accessions match, prefer the reviewed (Swiss-Prot) canonical entry for the intended organism; state which you chose.
3. Fetch details for a kept accession from the UniProt REST API, e.g. https://rest.uniprot.org/uniprotkb/<ACC>.json (or .txt/.fasta) for function, subcellular location, domains/features, cross-references, and sequence. Ask before large batch fetches.
4. Report the accession, protein and gene names, organism, and the requested annotation, with the entry URL.
5. Hand off cleanly: for 3D structure of an accession use $cx-alphafold-structure-analysis; for structural homologs use $cx-foldseek-structural-search.
6. Provenance & review: record queries, tool, and cited accessions with $science-provenance; check claims with $science-review before presenting.

Boundaries

• Cite only accessions actually returned by the tool; never invent accessions or annotation. Distinguish reviewed (Swiss-Prot) from unreviewed (TrEMBL) entries.
• Report the organism explicitly — gene names are ambiguous across species.
• This tool searches metadata; it does not align sequences or predict structure.