Uniprot MCP Server

@cyanheads/uniprot-mcp-server Search UniProtKB by protein function, fetch curated records, map IDs across databases, and pull reference proteomes, taxonomy, and sequences via MCP. STDIO or Streamable HTTP. Its README documents 6 tools, including uniprot_search_proteins, uniprot_get_entry, uniprot_map_ids.

People who work with bioinformatics, cyanheads and protein and want it reachable from Claude, Cursor, VS Code, or another MCP client. The project is written in TypeScript.

VERIFIED ACTIVE

LAST COMMIT 2026-09-20 · ★ 2 · #74 OF 174 MAINTAINED DATABASE · VERIFIED 2026-09-30

Apache-2.0 · TypeScript servers · how we verify → /methodology

01 · Install Uniprot MCP Server

before you install - you'll need

Set MCP_TRANSPORT_TYPE, MCP_LOG_LEVEL before connecting.

Claude Code

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

Claude Desktop / Cursor / VS Code - add to config

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

Same JSON for Cursor. For VS Code, rename the top-level key from `mcpServers` to `servers`.

Using another client? Same JSON, different key

Claude Desktop · mcpServers

Cursor · mcpServers

VS Code · servers

Windsurf · mcpServers

Zed · context_servers

Cline · mcpServers

Roo Code · mcpServers

Continue · mcpServers

LibreChat · mcpServers

Gemini CLI · mcpServers

Codex CLI · mcp_servers

Full setup guides: every client.

02 · Evidence

https://uniprot.caseyjhand.com/mcp

transport: streamable-http

endpoint alive - responded to MCP initialize · probed 2026-09-30

Security posture

What to check before giving this server access to your agent - from the registry, GitHub, and our own probes. We don't score safety; we show what's verifiable.

runs as local process (stdio) - runs on your machine with your user's permissions · remote - your agent's requests go to uniprot.caseyjhand.com

endpoint auth accepted our unauthenticated MCP initialize - no credentials needed to connect

license Apache-2.0 - declared in the repository

npm package @cyanheads/uniprot-mcp-server - published under the repo owner's npm scope (@cyanheads)

registry namespace io.github.cyanheads is GitHub-verified and matches the repo owner

03 · What Uniprot MCP Server can do

Prose above is summarized from the project's README and registry record - no invented capabilities.

What you can build

An agent gets 6 documented tools, including uniprot_search_proteins, uniprot_get_entry, uniprot_map_ids, uniprot_get_proteome, uniprot_get_taxonomy.

The 6 tools it gives your agent

Extracted from the project's README - what uniprot-mcp-server lets an agent do.

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-paginat
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
uniprot_map_ids: - Translate identifiers across databases via UniProt's async ID-mapping service - gene names, Ensembl, RefSeq, ChEMBL, PDB, GeneID ↔ UniProtKB accessions. Polls w
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

Latest releases

v0.2.4 · 2026-09-20

stateless session posture, mcp-ts-core ^0.13.6 · Session mode resolves to stateless on every launch path (#16) - createApp({ sessionMode: 'stateless' }) declares it in source and .env.example sets it actively, where…

v0.2.3 · 2026-08-30

Bounded UniProt ID mapping results · Preserve UniProt failedIds in unmappedIds and content output (#13) · Return one completed result page with a distinct continuation (#14) · Keep FINISHED status probes from following…

v0.2.2 · 2026-08-21

ValidationError contract codes and mcp-ts-core 0.12.3 · Eight typed contract errors return ValidationError (-32007) instead of InvalidParams (-32602), across uniprot_search_proteins, uniprot_map_ids…

04 · Who maintains Uniprot MCP Server

uniprot-mcp-server is maintained by cyanheads. We track 137 MCP servers from cyanheads - 131 actively maintained, 1,856 combined GitHub stars, oldest repo from Dec 2024. Full record: all servers from cyanheads.

05 · Facts

repository: github.com/cyanheads/uniprot-mcp-server
category: database - ranked #74 of 174 actively-maintained database servers as of 2026-09-30.
release cadence: 3 releases in the last 90 days (latest 2026-09-20)
registry: io.github.cyanheads/uniprot-mcp-server (active, first published 2026-06-28 · 5 versions)
packages: npm:@cyanheads/uniprot-mcp-server · npm:@cyanheads/uniprot-mcp-server

06 · Uniprot MCP Server FAQ

Is Uniprot MCP Server still maintained?

Yes - as of 2026-09-30, its last commit was 2026-09-20 and it shipped 3 releases in the last 90 days. We re-verify nightly.

What can Uniprot MCP Server do?

An agent gets 6 documented tools, including uniprot_search_proteins, uniprot_get_entry, uniprot_map_ids, uniprot_get_proteome, uniprot_get_taxonomy.

How do I install Uniprot MCP Server?

Run `npx -y @cyanheads/uniprot-mcp-server`. The README documents 2 environment variables (MCP_TRANSPORT_TYPE, MCP_LOG_LEVEL) to set first. Set MCP_TRANSPORT_TYPE, MCP_LOG_LEVEL before connecting. You can also paste the ready-made client config above.

Does Uniprot MCP Server require authentication?

No - the endpoint accepted our unauthenticated MCP initialize when probed on 2026-09-30; you can connect without credentials.

07 · Alternatives to Uniprot MCP Server

Alternatives to Uniprot MCP Server

Maintained database servers if Uniprot MCP Server isn't the fit.

More database MCP servers · Data Charter · Dbatools MCP Server · Dbtrail · Mcpg · ClickHouse

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