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io.github.cyanheads/uniprot-mcp-server

io.github.cyanheads/uniprot-mcp-server · v0.3.0

Measured by MCP Station

Description written by the publisher, not verified

Protein research over UniProtKB: search by function, fetch curated records, map IDs, proteomes.

Connect

claude mcp add --transport http uniprot-mcp-server https://uniprot.caseyjhand.com/mcp

{
  "mcpServers": {
    "uniprot-mcp-server": {
      "url": "https://uniprot.caseyjhand.com/mcp"
    }
  }
}

Tools as reported by the server

• uniprot_search_proteins
  Search UniProtKB and return curated protein records. Pass text_search for a plain-language query (the 80% case) or query for the full Lucene field syntax (gene:TP53 AND organism_id:9606 AND reviewed:true) — exactly one is required. Reviewed (Swiss-Prot) entries are manually curated; unreviewed (TrEM
• uniprot_get_entry
  Fetch full curated UniProtKB entries by accession in one batch (up to 20). Each entry carries function, catalytic activity, cofactors, subcellular location, disease involvement, PTMs, natural variants, isoforms, domains, GO terms, keywords, and cross-references. Partial failures do not abort the bat
• uniprot_map_ids
  Translate identifiers across databases via UniProt's ID-mapping service — gene names to accessions, accession to PDB / Ensembl / RefSeq / ChEMBL / GeneID, and back. The job runs asynchronously; this tool submits it and polls within a budget. A running job returns status "running" with a ticket; pass
• uniprot_get_proteome
  Fetch the reference proteome for an organism by UPID (e.g. "UP000005640") or NCBI taxon ID (e.g. 9606) — provide exactly one. Returns metadata inline: proteome type, total protein count, BUSCO completeness (score, complete/fragmented/missing counts, lineage dataset), and the genome assembly accessio
• uniprot_get_taxonomy
  Resolve a taxonomy record by NCBI taxon ID (e.g. 9606) or scientific name (e.g. "Homo sapiens") — provide exactly one. Returns the scientific and common name, mnemonic, rank, parent, and the full lineage. Set include_children to also fetch immediate child taxa (a separate lookup — not inline on the
• uniprot_get_sequence
  Fetch the canonical amino-acid sequence (FASTA) for a UniProtKB accession, with length and the parsed header. Set include_isoforms to also return the alternatively-spliced isoform sequences. This is the cheap sequence-only path — for the full functional record use uniprot_get_entry. A merged accessi

Tool changes

• 2026-10-23: uniprot_search_proteins, uniprot_get_entry, uniprot_map_ids, uniprot_get_proteome, uniprot_get_taxonomy, uniprot_get_sequence
• 2026-10-16: uniprot_search_proteins, uniprot_get_entry, uniprot_map_ids, uniprot_get_proteome, uniprot_get_taxonomy, uniprot_get_sequence

Repository · JSON · Text for agents · Registry updated 2026-10-22