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UniProt MCP Server

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Overview

The UniProt MCP Server is a Model Context Protocol (MCP) server that provides access to UniProt protein information, allowing AI assistants to fetch protein function and sequence information directly from UniProt.

To use the UniProt MCP Server, clone the repository, install the required dependencies, and configure it in your Claude Desktop application. You can then query protein information using UniProt accession numbers.

  • Retrieve protein information by UniProt accession number - Batch retrieval of multiple proteins - Caching for improved performance (24-hour TTL) - Detailed error handling and logging - Information provided includes protein name, function description, full sequence, sequence length, and organism.
  1. Fetching detailed information about specific proteins for research purposes.
  2. Comparing multiple proteins' information for analysis.
  3. Integrating protein data into AI applications for enhanced functionality.

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

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

Claude Code

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

.mcp.json (project root)

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

VS Code (Copilot)

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

.vscode/mcp.json

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

Windsurf

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

~/.codeium/windsurf/mcp_config.json

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

Cline

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

Cline MCP Settings (via UI)

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

FAQ

Can I retrieve information for multiple proteins at once?

Yes! The server supports batch retrieval of protein information.

What programming language is required to run the server?

You need Python 3.10 or higher to run the UniProt MCP Server.

Is there any caching mechanism in place?

Yes, the server implements caching with a 24-hour time-to-live (TTL) for improved performance.7:["$","div",null,{"className":"container mx-auto flex flex-col gap-4","children":["$L26","$L27",["$","$L28",null,{"currentProject":{"id":706,"uuid":"3ac1762b-1318-4d26-aa2f-7d6b82710a7e","name":"TakumiY235_uniprot-mcp-server","title":"UniProt MCP Server","description":"Mirror of","avatar_url":"https://avatars.githubusercontent.com/u/192820360?v=4","created_at":"2024-12-30T03:26:54.154+00:00","updated_at":"2025-02-23T07:16:03.124+00:00","status":"created","author_name":"MCP-Mirror","author_avatar_url":"https://avatars.githubusercontent.com/u/192820360?v=4","tags":"uniprot,mcp-server,protein-information","category":"research-and-data","is_featured":false,"sort":1,"url":"https://github.com/MCP-Mirror/TakumiY235_uniprot-mcp-server","target":"_self","content":"$29","summary":"$2a","img_url":null,"type":null,"metadata":null,"user_uuid":null,"tools":null,"sse_url":null,"sse_provider":null,"sse_params":null,"is_official":false,"server_command":null,"server_params":null,"server_config":null,"allow_call":false,"is_innovation":false,"is_dxt":false,"dxt_manifest":null,"dxt_file_url":null,"is_audit":false},"randomProjects":[],"currentServerKey":"$undefined"}]]}]

Research and data
UniProt MCP Server — MCP Registry