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UniProt MCP Server

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MCP server for UniProt protein data access

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Overview

UniProt MCP Server is a backend service that provides access to UniProt protein information, enabling AI assistants to fetch protein function and sequence details directly from UniProt.

To use the UniProt MCP Server, clone the repository, install dependencies, and configure the server in the Claude Desktop application. Use API queries to request protein information based on accession numbers.

  • Retrieve protein information using UniProt accession numbers - Batch retrieval for multiple proteins - Performance caching with 24-hour TTL - Comprehensive error handling and logging
  1. Accessing protein data for bioinformatics analyses
  2. Integrating protein queries into AI-driven applications
  3. Comparing multiple protein sequences and functions in research workflows

Add to your AI client

Use these steps to connect UniProt MCP Server in Cursor, Claude, VS Code, and other MCP-compatible apps. The same JSON appears in the Use with menu above for one-click copy.

Cursor

Add this to your .cursor/mcp.json file in your project root, then restart Cursor.

.cursor/mcp.json

{
  "mcpServers": {
    "uniprot-mcp-server-takumiy235": {
      "command": "npx",
      "args": [
        "-y",
        "@modelcontextprotocol/server-uniprot-mcp-server-takumiy235"
      ]
    }
  }
}

Claude Desktop

Add this server entry to the mcpServers object in your Claude Desktop config, then restart the app.

~/Library/Application Support/Claude/claude_desktop_config.json (macOS) or %APPDATA%\Claude\claude_desktop_config.json (Windows)

{
  "mcpServers": {
    "uniprot-mcp-server-takumiy235": {
      "command": "npx",
      "args": [
        "-y",
        "@modelcontextprotocol/server-uniprot-mcp-server-takumiy235"
      ]
    }
  }
}

Claude Code

Add this to your project's .mcp.json file. Claude Code will detect it automatically.

.mcp.json (project root)

{
  "mcpServers": {
    "uniprot-mcp-server-takumiy235": {
      "command": "npx",
      "args": [
        "-y",
        "@modelcontextprotocol/server-uniprot-mcp-server-takumiy235"
      ]
    }
  }
}

VS Code (Copilot)

Add this to your .vscode/mcp.json file. Requires the GitHub Copilot extension with MCP support enabled.

.vscode/mcp.json

{
  "servers": {
    "uniprot-mcp-server-takumiy235": {
      "type": "stdio",
      "command": "npx",
      "args": [
        "-y",
        "@modelcontextprotocol/server-uniprot-mcp-server-takumiy235"
      ]
    }
  }
}

Windsurf

Add this to your Windsurf MCP config file, then restart Windsurf.

~/.codeium/windsurf/mcp_config.json

{
  "mcpServers": {
    "uniprot-mcp-server-takumiy235": {
      "command": "npx",
      "args": [
        "-y",
        "@modelcontextprotocol/server-uniprot-mcp-server-takumiy235"
      ]
    }
  }
}

Cline

Open Cline settings, navigate to MCP Servers, and add this server configuration.

Cline MCP Settings (via UI)

{
  "mcpServers": {
    "uniprot-mcp-server-takumiy235": {
      "command": "npx",
      "args": [
        "-y",
        "@modelcontextprotocol/server-uniprot-mcp-server-takumiy235"
      ]
    }
  }
}

FAQ

What types of data can I retrieve?

You can retrieve protein name, function description, full sequence, sequence length, and organism.

Is it easy to configure for use?

Yes, the server setup involves simple configuration steps in your local environment.

Can I handle errors when making requests?

Yes, the server includes detailed error handling for various scenarios like invalid accession numbers and network issues.

Research and data