How to Use the UniProt MCP in Claude Code

Q: How do I query UniProt using Claude Code?

You execute searchuniprot directly in the terminal. You can pass keywords like 'spike protein' and pipe the returned list of proteins into another tool for analysis or logging.

Q: Can I use UniProt to get details on a specific accession ID with Claude Code?

Yes, simply run getuniprotprotein and pass in the ID. The output gives you all the necessary protein data—sequences, locations, everything—right to standard out.

Q: If I need to find isoforms using UniProt with Claude Code, what command runs?

Use searchuniprotgene. This tool returns every protein isoform and its functional annotations for a specific gene. The output is perfect for scripting loops or generating structured data files.

Automate biological research pipelines with Claude Code and UniProt MCP Server.

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Connect UniProt MCP to Claude Code

Create your Vinkius account to connect UniProt to Claude Code 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 Code

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Fetch full protein data for CI/CD scripting.

To get all details on a single protein, pipe the result of `get_uniprot_protein` into your script. This tool pulls comprehensive information—including subcellular location and sequence—making it perfect for automated reporting.

Run large-scale UniProt searches in headless mode.

You can run `search_uniprot` from a cron job to query thousands of proteins using names or functions. The output feeds directly into your shell script for further processing, like generating CSV reports.

Process gene-to-protein mapping in pipelines.

For automated workflows, `search_uniprot_gene` returns a list of all protein isoforms and their functional notes. This list can be captured by your shell script for batch processing or database ingestion.

Setup guide

Set up UniProt MCP in Claude Code

Prerequisites

Claude Code CLI installed (npm install -g @anthropic-ai/claude-code)
Active Vinkius subscription with a valid endpoint token

1

Run the add command

Open your terminal and run the command shown on the right. Replace [YOUR_TOKEN_HERE] with your endpoint token from cloud.vinkius.com. Use --scope user to make it available across all projects.
2

Verify the connection

Start a Claude Code session and type /mcp to list connected servers. You should see uniprot-mcp with a green status indicator.
3

Start using tools

Ask Claude Code something like "Check my latest UniProt transactions." It will automatically discover and invoke the available UniProt tools.

Terminal

claude mcp add --transport http uniprot-mcp https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp

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Prerequisites

Claude Code CLI installed
Active Vinkius subscription with a valid endpoint token

1

Open the config file

Create or edit .mcp.json in your project root for project-level scope, or ~/.claude.json for user-level scope.
2

Add the UniProt MCP

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

Restart Claude Code

Start a new Claude Code session. Type /mcp to confirm the server is connected. The tools will be automatically available in your conversation.

.mcp.json

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

Get your connection token →

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Common questions about UniProt MCP in Claude Code

You execute `search_uniprot` directly in the terminal. You can pass keywords like 'spike protein' and pipe the returned list of proteins into another tool for analysis or logging.

Yes, simply run `get_uniprot_protein` and pass in the ID. The output gives you all the necessary protein data—sequences, locations, everything—right to standard out.

UniProt supports searching by name, function, or keyword via `search_uniprot`. This is great for CI/CD pipelines that need to validate protein existence across a wide range of inputs.

The server only interacts with publicly available amino acid data, functional annotations, and protein sequences from the global UniProt knowledge base. No private records are accessed.

Use `search_uniprot_gene`. This tool returns every protein isoform and its functional annotations for a specific gene. The output is perfect for scripting loops or generating structured data files.

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