> ## Documentation Index
> Fetch the complete documentation index at: https://docs.tamarind.bio/llms.txt
> Use this file to discover all available pages before exploring further.

# MCP Server

> Connect AI assistants to Tamarind tools

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"

## Requirements

To use Tamarind's MCP server, you need:

1. A Tamarind account - [Sign up here](https://app.tamarind.bio)
2. OAuth credentials or API key - Email [info@tamarind.bio](mailto:info@tamarind.bio) to request access
3. A compatible MCP client - Such as Claude, VS Code, ChatGPT, or other MCP-compatible tools

The Tamarind MCP server is available at `https://mcp.tamarind.bio/mcp`.

## Authentication

Tamarind MCP server supports two authentication methods:

### OAuth 2.1

OAuth authentication provides user-specific access control and is the recommended method for most users. View your OAuth credentials at [app.tamarind.bio/api-docs/mcp-server](https://app.tamarind.bio/api-docs/mcp-server) or email [info@tamarind.bio](mailto:info@tamarind.bio) to request access.

### API Key

API key authentication is a simpler alternative suitable for personal use or automation. View your API key at [app.tamarind.bio/api-docs/api-key](https://app.tamarind.bio/api-docs/api-key) or email [info@tamarind.bio](mailto:info@tamarind.bio) to request access.

## Connecting to Claude.ai (Web)

Claude.ai provides the simplest way to connect to Tamarind's MCP server with no installation required.

### Prerequisites

* Claude.ai account (free or paid)
* OAuth credentials from Tamarind

### Setup Steps

1. Go to [claude.ai](https://claude.ai)
2. Click on your profile icon → **Settings**
3. Navigate to **Integrations** or **Connectors**
4. Click **Add Connector** or **Add Integration**
5. Fill in the connector details:
   * **Name**: `Tamarind`
   * **Server URL**: `https://mcp.tamarind.bio/mcp`
   * **Authentication**: Select OAuth 2.1
   * **Authorization URL**: `https://clerk.tamarind.bio/oauth/authorize`
   * **Token URL**: `https://clerk.tamarind.bio/oauth/token`
   * **Client ID**: Your Tamarind OAuth client ID
   * **Client Secret**: Your Tamarind OAuth client secret
   * **Scopes**: `openid email profile`
6. Click **Connect** or **Save**
7. You'll be redirected to authenticate with your Tamarind account
8. Authorize the connection

Once connected, you can use Tamarind tools directly in your Claude.ai conversations!

## Connecting to Claude Desktop

Claude Desktop provides native support for MCP servers with both OAuth and API key authentication.

### API Key Authentication

1. Get your API key from [app.tamarind.bio/api-docs/api-key](https://app.tamarind.bio/api-docs/api-key) or email [info@tamarind.bio](mailto:info@tamarind.bio)
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:

```json theme={null}
{
  "mcpServers": {
    "tamarind": {
      "command": "npx",
      "args": [
        "mcp-remote",
        "https://mcp.tamarind.bio/mcp",
        "--header",
        "x-api-key:YOUR_API_KEY_HERE"
      ]
    }
  }
}
```

4. Restart Claude Desktop

Once connected, you'll see Tamarind appear in your connectors list.

### OAuth Authentication

1. Get your OAuth credentials from [app.tamarind.bio/api-docs/mcp-server](https://app.tamarind.bio/api-docs/mcp-server)
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:

```json theme={null}
{
  "mcpServers": {
    "tamarind": {
      "command": "npx",
      "args": [
        "mcp-remote",
        "https://mcp.tamarind.bio/mcp",
        "--static-oauth-client-info",
        "{\"client_id\":\"CLIENT_ID\",\"client_secret\":\"CLIENT_SECRET\"}",
        "--callback-port",
        "3334"
      ]
    }
  }
}
```

4. Restart Claude Desktop
5. The first time you use Tamarind tools, you'll be prompted to authenticate in your browser
6. Log in with your Tamarind account

Once connected, you'll see Tamarind appear in your connectors list.

## Connecting to VS Code

VS Code supports MCP servers through GitHub Copilot Chat. Configure OAuth authentication in your `mcp.json` file with the server URL `https://mcp.tamarind.bio/mcp` and the OAuth endpoints from Tamarind. You can then use `@tamarind` in Copilot Chat to access Tamarind tools.

Refer to the [VS Code MCP documentation](https://code.visualstudio.com/docs/copilot/reference/mcp-configuration) for detailed setup instructions.

## Connecting to ChatGPT

ChatGPT supports MCP servers through Developer Mode (available to Plus, Pro, Business, and Enterprise users). Create a custom app in ChatGPT Settings with the Tamarind MCP server URL and OAuth credentials. Once configured, you can use Tamarind tools directly in ChatGPT conversations.

Refer to the [ChatGPT Developer Mode documentation](https://help.openai.com/en/articles/12584461-developer-mode-apps-and-full-mcp-connectors-in-chatgpt-beta) for detailed setup instructions.

## Connecting to Codex (OpenAI)

Codex supports remote MCP servers with API key authentication.

### Prerequisites

* Codex installed ([Install Codex](https://developers.openai.com/codex))
* API key from [app.tamarind.bio/api-docs/api-key](https://app.tamarind.bio/api-docs/api-key)

### Setup Steps

1. Set your API key as an environment variable in your shell profile (`~/.zshrc` or `~/.bashrc`):

```bash theme={null}
export TAMARIND_API_KEY="your-api-key-here"
```

2. Add the following to `~/.codex/config.toml`:

```toml theme={null}
[mcp_servers.tamarind]
url = "https://mcp.tamarind.bio/mcp"
env_http_headers = { "x-api-key" = "TAMARIND_API_KEY" }
```

3. Launch Codex and use Tamarind tools directly.

## Connecting to Other MCP Clients

Other MCP-compatible clients like Cursor, Windsurf, or custom implementations can connect to the Tamarind MCP server at `https://mcp.tamarind.bio/mcp` using either OAuth or API key authentication, depending on what the client supports.

Refer to your specific MCP client's documentation for configuration details. If you need help setting up a specific MCP client, email [info@tamarind.bio](mailto:info@tamarind.bio) and we'll work with you to get it supported.

## Available Tools

The Tamarind MCP server provides access to the following capabilities:

| Tool            | Description                                    |
| --------------- | ---------------------------------------------- |
| **submitJob**   | Submit individual computational jobs           |
| **submitBatch** | Submit batch jobs with multiple configurations |
| **getJobs**     | Retrieve job status and metadata               |
| **getResult**   | Download results from completed jobs           |
| **uploadFile**  | Upload input files (PDB, FASTA, etc.)          |
| **getFiles**    | View your uploaded input files                 |

Each tool corresponds to the REST API endpoints documented in our [full API reference](https://app.tamarind.bio/api-docs).

## Troubleshooting

### Connector not appearing

* Save configuration file in the correct location and restart your client
* Verify JSON syntax is correct (no missing commas or brackets)

### Authentication failing

* Verify your credentials (client ID/secret or API key) are correct
* For OAuth: Log in with your Tamarind account and try again if timeout occurs

### Changes not applying

* Save the file, then completely quit and restart your client (not just refresh)

### Tools not working

* Verify your authentication is still valid and try reconnecting

Need help? Contact us at [info@tamarind.bio](mailto:info@tamarind.bio)

## Related Resources

* [Full API Documentation](https://app.tamarind.bio/api-docs) - Complete REST API reference
* [API Overview](/tamarind/api) - Getting started with Tamarind's API
* [Batch Jobs](/tamarind/batch) - Running batch computations
* [Manage Team](/support/manage-team) - Team settings and permissions