How to Use the UniProt MCP in Claude

Q: Can I use UniProt to find a protein by name in Claude Desktop?

Yep. You just call the searchuniprot tool. It lets you search broadly using common names or keywords like 'hemoglobin' to get a list of matching candidates.

Pull complex protein data straight into your Claude Desktop chat, without leaving the app.

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Connect UniProt MCP to Claude Desktop

Create your Vinkius account to connect UniProt to Claude Desktop and route execution through our secure gateway. The platform manages server hosting, runtime updates, and security layers. Configuration requires no manual server provisioning.

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Setup UniProt with Claude Desktop

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Search UniProt via MCP Server

Need to find proteins by keyword or function? You can run `search_uniprot` against the 250M+ sequence database. Just input a query like 'insulin' or 'p53,' and you get back protein name, gene info, organism, location, and the full amino acid sequence. This is perfect for when your agent needs to pull background context for a research report—it doesn't require leaving Claude Desktop to hit an external API.

Get Protein Details with `get_uniprot_protein`

If you already have the UniProt accession ID, use `get_uniprot_protein`. This tool pulls every detail associated with that specific protein record. You get everything: function annotations, subcellular location, and comprehensive structural data. It’s a direct lookup; no fuzzy searching needed. Just give it the ID, and your agent handles the rest of the heavy lifting.

Find Proteins from Gene Using MCP Server

Sometimes you start with a gene name instead of a protein. The `search_uniprot_gene` tool solves that by returning all possible protein isoforms and their functional annotations for a given gene. You don't have to guess which transcript is correct. This feature really shines when mapping out biological pathways, letting your agent systematically check every potential product from a specific locus.

Setup guide

Set up UniProt MCP in Claude Web or Desktop

1

Open Claude Settings

Go to claude.ai, click your profile icon, then navigate to Customize → Connectors.
2

Add Custom Connector

Click the "+" button and select Add custom connector. Paste your Vinkius endpoint URL: https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp Replace [YOUR_TOKEN_HERE] with your token from cloud.vinkius.com. For OAuth-protected servers, expand Advanced settings to add credentials.
3

Start a conversation

Open a new chat. The UniProt MCP tools are available immediately — no restart needed.

Endpoint URL

https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp

No configuration file needed — paste the URL directly in the Claude web interface.

Available on Free (1 connector), Pro, Max, Team, and Enterprise plans.

Prerequisites

Claude Desktop installed (macOS or Windows)
Active Vinkius subscription with a valid endpoint token

1

Open Claude Desktop Settings

Click the menu icon at the top-left corner, go to Settings → Developer → Edit Config. This opens claude_desktop_config.json in your default text editor.
2

Paste the UniProt MCP configuration

Copy the JSON snippet on the right into the mcpServers object. Replace [YOUR_TOKEN_HERE] with your endpoint token from cloud.vinkius.com.
3

Restart Claude Desktop

Close and reopen the application. Claude needs a full restart to load new MCPs — refreshing a conversation is not enough.
4

Verify the connection

Open a new conversation. Click the 🔌 icon at the bottom of the message input. You should see tools listed under uniprot-mcp.

json

{
  "mcpServers": {
    "uniprot-mcp": {
      "url": "https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp"
    }
  }
}

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Independent Platform Disclaimer: Vinkius is an independent platform and is not affiliated with, endorsed by, sponsored by, verified by, or otherwise authorized by UniProt. All third-party trademarks, logos, and brand names are the property of their respective owners. Their use on this website is strictly for informational purposes to identify service compatibility and interoperability.

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Common questions about UniProt MCP in Claude Desktop

You connect the MCP Server via Settings → Integrations. Once linked in Claude Desktop, your agent can invoke tools like `search_uniprot` directly when you ask a question.

This server accesses publicly available protein sequences and functional annotations. The specific data types involved are UniProt accession IDs, amino acid data, and organism information.

Yep. You just call the `search_uniprot` tool. It lets you search broadly using common names or keywords like 'hemoglobin' to get a list of matching candidates.

UniProt provides highly structured, curated data—it includes subcellular location and detailed functional annotations alongside the sequence. It’s much more specific than just a raw sequence dump.

No, you just have to fully restart the Claude Desktop application for the new local MCP Server configuration to take effect. The web version requires simply re-authenticating the connector.

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