MCP server

Uniprot

io.github.cyanheads/uniprot-mcp-server

Checked 26 Oct 2026, 08:29 UTC · Connected to it and listed its tools

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

Source

At a glance

Type

MCP server

Publisher

Not verified

Status

Working at last check

Tools

6

Token cost

About 4,149 tokens per request

Sets up in

Claude Code, Claude Desktop, Codex, Gemini CLI, Cursor, VS Code, Antigravity, ChatGPT, OpenAI API, Grok

Last checked

26 Oct 2026, 08:29 UTC

Connect it to your agent

Add to CursorAdd to VS CodeVS Code Insiders

Opens the app, which shows the server and asks you to confirm. For other apps, copy the setup below.

Claude Code

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

Claude Desktop

Settings → Connectors → Add custom connector, and paste the URL.

Codex (config.toml)

[mcp_servers.uniprot-mcp-server]
url = "https://uniprot.caseyjhand.com/mcp"

Gemini CLI

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

Cursor

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

VS Code

{"servers":{"uniprot-mcp-server":{"type":"http","url":"https://uniprot.caseyjhand.com/mcp"}}}

Antigravity

agy mcp add uniprot-mcp-server https://uniprot.caseyjhand.com/mcp

ChatGPT

Settings → Apps & Connectors → Advanced settings: turn on Developer mode, then Create a connector and paste the URL. Which plans can do this varies.

OpenAI API (Responses tools)

{"type":"mcp","server_label":"uniprot-mcp-server","server_url":"https://uniprot.caseyjhand.com/mcp","require_approval":"always"}

Grok (xAI API tools)

{"type":"mcp","server_label":"uniprot-mcp-server","server_url":"https://uniprot.caseyjhand.com/mcp"}

Tools

• uniprot_get_entry ~964 tokens
  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_get_proteome ~578 tokens
  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_sequence ~353 tokens
  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
• uniprot_get_taxonomy ~416 tokens
  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_map_ids ~949 tokens
  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_search_proteins ~889 tokens
  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

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