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Tamarind offers a Model Context Protocol (MCP) server that allows AI assistants and other applications to access Tamarind’s computational biology tools. With the MCP server, you can:
  • Submit protein design and structure prediction jobs
  • Query job status and retrieve results
  • Upload and manage input files
  • Access all Tamarind tools through natural language
For example, you could ask your AI assistant:
  • “Submit an RFDiffusion job to design a binder for this target protein”
  • “Check the status of my recent structure prediction jobs”
  • “Get the results from my batch antibody design job”

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Requirements

To use Tamarind’s MCP server, you need:
  1. A Tamarind account - Sign up here
  2. A Tamarind API key - View your key at app.tamarind.bio/api-docs/api-key or email info@tamarind.bio to request access
  3. A compatible MCP client - Such as Claude Desktop, VS Code, or other MCP-compatible tools
The Tamarind MCP server is available at https://mcp.tamarind.bio/mcp. You can list all available tools by using the tools/list MCP command through your MCP client.

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Connecting to Claude

Claude Desktop provides native support for MCP servers. To connect Tamarind:
  1. Get your API key from app.tamarind.bio/api-docs/api-key (email info@tamarind.bio to request access if needed)
  2. Open your Claude Desktop configuration file:
    • macOS: ~/Library/Application Support/Claude/claude_desktop_config.json
    • Windows: %APPDATA%\Claude\claude_desktop_config.json
  3. Add the Tamarind MCP server:
{
  "mcpServers": {
    "tamarind": {
      "command": "npx",
      "args": [
        "mcp-remote",
        "https://mcp.tamarind.bio/mcp",
        "--header",
        "x-api-key:YOUR_API_KEY_HERE"
      ]
    }
  }
}
  1. Restart Claude Desktop
Once connected, you’ll see Tamarind appear in your connectors list.

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Connecting to other MCP clients

For other MCP-compatible clients like Cursor, VS Code, Windsurf, or custom implementations, use the same configuration format: 
{
  "mcpServers": {
    "tamarind": {
      "command": "npx",
      "args": [
        "mcp-remote",
        "https://mcp.tamarind.bio/mcp",
        "--header",
        "x-api-key:YOUR_API_KEY_HERE"
      ]
    }
  }
}
The configuration uses npx mcp-remote to connect to the Tamarind MCP server. The mcp-remote package will be automatically installed when your MCP client starts. Refer to your specific MCP client’s documentation for configuration details.

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Available tools

The Tamarind MCP server provides access to the following capabilities:
ToolDescription
submit-jobSubmit individual computational jobs
submit-batchSubmit batch jobs with multiple configurations
get-jobsRetrieve job status and metadata
get-resultsDownload results from completed jobs
upload-fileUpload input files (PDB, FASTA, etc.)
list-filesView your uploaded input files
Each tool corresponds to the REST API endpoints documented in our full API reference.

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Authentication

All requests require a Tamarind API key. View your key at app.tamarind.bio/api-docs/api-key or email info@tamarind.bio to request access. Include your API key in your MCP client configuration as: x-api-key:YOUR_API_KEY_HERE Need help? Contact us at info@tamarind.bio