How do I install Uniprot?

Uniprot is a remote plugin. You do not need to install anything locally. Add the server URL to your AI app's MCP configuration and you are ready to go.

Is Uniprot safe to use?

Yes. Uniprot passed MCP Marketplace's automated security scan with a score of 10/10 (low risk). Every server on MCP Marketplace is security-scanned before it's listed; see the full security report on this page for the findings and permissions.

What AI apps work with Uniprot?

Uniprot uses the Model Context Protocol (MCP) and works with any MCP-compatible AI app, including Claude, ChatGPT / Codex, Gemini, Copilot, Cursor, and more.

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Uniprot MCP Server

by Pipeworx Io

Developer ToolsLow Risk10.0MCP RegistryRemote

Free

Server data from the Official MCP Registry

UniProt MCP — protein sequence + function database.

About

UniProt MCP — protein sequence + function database.

Remote endpoints: streamable-http: https://gateway.pipeworx.io/uniprot/mcp

Security Report

10.0

Low Risk10.0Low Risk

Valid MCP server (1 strong, 0 medium validity signals). No known CVEs in dependencies. Imported from the Official MCP Registry. Trust signals: trusted author (1062/1065 approved). 1 finding(s) downgraded by scanner intelligence.

36 tools verified · Open access · 1 issue found

Security scores are indicators to help you make informed decisions, not guarantees. Always review permissions before connecting any MCP server.

Permissions Required

This plugin requests these system permissions. Most are normal for its category.

file_system

Check that this permission is expected for this type of plugin.

HTTP Network Access

Connects to external APIs or services over the internet.

How to Connect

Remote Plugin

No local installation needed. Your AI client connects to the remote endpoint directly.

Add this to your MCP configuration to connect:

{
  "mcpServers": {
    "io-github-pipeworx-io-uniprot": {
      "url": "https://gateway.pipeworx.io/uniprot/mcp"
    }
  }
}

Documentation

View on GitHub

From the project's GitHub README.

mcp-uniprot

UniProt MCP — protein sequence + function database.

Part of Pipeworx — an MCP gateway connecting AI agents to 965+ live data sources.

Tools

Tool	Description
`search`	"Find protein [name]" / "look up [gene] in UniProt" / "BRCA1 / TP53 / insulin protein info" / "all proteins for [organism]" — UniProtKB search via Lucene-style queries (e.g. "gene:BRCA1 AND organism_id:9606" for human BRCA1). UniProt is the authoritative protein-sequence-and-function database — use for protein characterization, function annotation, sequence retrieval, and cross-references to PDB/GO/PubMed.
`get`	"Fetch protein [P12345]" / "UniProt entry for [accession]" / "FASTA sequence for [protein]" — single UniProtKB entry by accession (e.g. P12345 or P38398 for BRCA1_HUMAN). Returns full protein record: sequence, function annotations, GO terms, cross-refs, post-translational modifications, variants. Pass format=fasta for sequence only.
`proteomes_search`	"Reference proteome for [organism]" / "complete protein set of [species]" — search UniProt reference proteomes (the curated representative protein set per organism). Use as a starting point for genome-scale protein analyses.
`taxonomy_search`	"NCBI taxonomy ID for [organism]" / "taxid for [species]" / "look up [Latin name] in NCBI taxonomy" — search NCBI Taxonomy via UniProt's mirror. Returns taxonomic IDs you can use as organism_id filters in `search` (9606 = human, 10090 = mouse, 7227 = D. melanogaster, etc).
`keyword`	"UniProt keyword KW-N info" / "what does keyword [X] mean" — fetch a UniProt controlled-vocabulary keyword by ID. Use to look up annotation tags like "Kinase" / "Membrane" / "Disease-associated".
`feature_summary`	"Domain map of [protein]" / "annotated features of [accession]" / "what regions / sites does [protein] have" — annotated features (domains, active sites, transmembrane regions, mutagenesis sites, glycosylation, disulfide bonds, etc.) for a UniProt accession. Use for structural/functional analysis without pulling the full protein record.

Quick Start

Add to your MCP client (Claude Desktop, Cursor, Windsurf, etc.):

{
  "mcpServers": {
    "uniprot": {
      "url": "https://gateway.pipeworx.io/uniprot/mcp"
    }
  }
}

Or connect to the full Pipeworx gateway for access to all 965+ data sources:

{
  "mcpServers": {
    "pipeworx": {
      "url": "https://gateway.pipeworx.io/mcp"
    }
  }
}

Using with ask_pipeworx

Instead of calling tools directly, you can ask questions in plain English:

ask_pipeworx({ question: "your question about Uniprot data" })

The gateway picks the right tool and fills the arguments automatically.

License

MIT

Reviews

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Uniprot MCP Server

About

Security Report

Findings (1)

Permissions Required

How to Connect

Documentation

mcp-uniprot

Tools

Quick Start

Using with ask_pipeworx

More

License

Reviews

No reviews yet

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