Search UniProtKB by protein function, fetch curated records, map IDs across databases, and pull reference proteomes, taxonomy, and sequences via MCP.
Search UniProtKB by protein function, fetch curated records, map IDs across databases, and pull reference proteomes, taxonomy, and sequences via MCP. STDIO or
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Check the linked publisher documentation and your connected client's tool list. Names and availability can vary with the server version and account permissions.
| Tool | What it does |
|---|---|
| uniprot_search_proteins | Search UniProtKB by plain text or a Lucene field query, with the reviewed (Swiss-Prot) filter foregrounded and optional server-side facet counts. Cursor-paginated. The discovery entry point. |
| uniprot_get_entry | Fetch full curated entries by accession in one batch (up to 20) — function, catalytic activity, disease, variants, isoforms, GO terms, cross-references. Partial-success output; an oversized record returns a section outli |
| uniprot_map_ids | Translate identifiers across databases via UniProt's async ID-mapping service — gene names, Ensembl, RefSeq, ChEMBL, PDB, GeneID ↔ UniProtKB accessions. Polls within a budget; returns a resumable ticket on overflow. |
| uniprot_get_proteome | Fetch a reference proteome by UPID or NCBI taxon ID — protein count, BUSCO completeness, genome assembly inline, plus an opt-in capped page of the proteins. |
| uniprot_get_taxonomy | Resolve a taxonomy record by NCBI taxon ID or scientific name — name, rank, parent, full lineage, and optionally the immediate children. |
| uniprot_get_sequence | Fetch the canonical amino-acid sequence (FASTA) for an accession, with length and parsed header — and optionally the isoform sequences. The cheap sequence-only path. |
{
"mcpServers": {
"uniprot-mcp-server": {
"type": "stdio",
"command": "bunx",
"args": ["@cyanheads/uniprot-mcp-server@latest"],
"env": {
"MCP_TRANSPORT_TYPE": "stdio",
"MCP_LOG_LEVEL": "info"
}
}
}
}Configuration as documented by the project. Restart the client after saving.
| Variable | Description | Required |
|---|---|---|
| MCP_TRANSPORT_TYPE | Configuration value read at startup. | Optional |
| MCP_LOG_LEVEL | Configuration value read at startup. | Optional |
| UNIPROT_BASE_URL | Endpoint or connection string the server talks to. | Yes |
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