Connect to the Biohub MCP and run your first query

Add Biohub MCP to your AI agent

Run claude --version to check that you have Claude Code 2.1.81 or later.

claude mcp add --transport http biohub https://biohub.ai/mcp

Add --scope user to make it available in every project. Start a new claude session, enter /mcp, select biohub, and choose to sign in. To check the connection later, enter /mcp or run claude mcp get biohub.

Run codex --version to check that you have Codex 0.148.0 or later. Older versions also connect, with a different sign-in method that Biohub MCP accepts.

codex mcp add biohub --url https://biohub.ai/mcp

Codex opens the sign-in page in your browser right away. If it does not, run codex mcp login biohub. Start a new codex session to use it. Run codex mcp list, or enter /mcp in a Codex session, to check that biohub is connected.The command writes this entry to ~/.codex/config.toml, which you can also add by hand:

[mcp_servers.biohub]
url = "https://biohub.ai/mcp"

If you add it by hand, run codex mcp login biohub to sign in.The ChatGPT desktop app and the Codex IDE extension share this configuration, so biohub appears there too. To add it from the ChatGPT desktop app instead, open Settings, then MCP servers, select Add server, enter biohub as the name, select Streamable HTTP, enter https://biohub.ai/mcp, save, and select Restart. Type /mcp in the composer to see the connected servers. This is separate from the developer-mode apps you add in ChatGPT on the web. See the Codex MCP documentation for more options.

These steps work in Claude.ai and Claude Desktop, which share your account’s connectors, so adding Biohub once covers both.

Open Customize, then Connectors.
Click +, then Add custom connector.
Enter Biohub as the name and https://biohub.ai/mcp as the remote MCP server URL.
If Claude asks which OAuth client to use, choose Use Claude’s published identity, and leave any client ID and secret fields empty.
Click Add, then Connect.
In a chat, click +, select Connectors, and turn on Biohub.

On Team and Enterprise plans, only an Owner can add a custom connector, under Organization settings, then Connectors, choosing Use Claude’s published identity. Members then click Connect under Customize, then Connectors, and each signs in with their own Biohub account. Free plans allow one custom connector.

Developer mode is available on the web for Plus, Pro, Business, Enterprise, and Education accounts. On a workspace plan, an admin may need to allow it.

In ChatGPT on the web, open Settings, then Security and login, and turn on Developer mode.
Open chatgpt.com/plugins and click + to create a developer-mode app for a remote MCP server.
Enter Biohub as the name and https://biohub.ai/mcp as the MCP server URL, select OAuth, leave any client ID and secret fields empty, and create it.
In a chat, select Developer mode from the + menu and select Biohub.

For the ChatGPT desktop app, use the Codex tab.

Add this entry to ~/.cursor/mcp.json for all projects, or to .cursor/mcp.json in one project, keeping any servers already listed there. You can also add the URL in Cursor Settings, then MCP.

{
  "mcpServers": {
    "biohub": {
      "url": "https://biohub.ai/mcp"
    }
  }
}

In Cursor Settings, then MCP, click Login or Connect next to biohub. When it’s connected, its tools are listed there; restart Cursor if it does not pick up the change.

VS Code uses MCP servers in Copilot Chat. If your organization manages GitHub Copilot, its policy must allow MCP servers.Run MCP: Add Server from the Command Palette and follow the prompts, or add this entry to .vscode/mcp.json in your workspace, keeping any servers already listed there:

{
  "servers": {
    "biohub": {
      "type": "http",
      "url": "https://biohub.ai/mcp"
    }
  }
}

To add it for your user profile instead, run MCP: Open User Configuration and add the same entry. Start the biohub server from the MCP view or the configuration file, and sign in when asked. Run MCP: List Servers to see its status, and select Configure Tools in Chat to turn the Biohub tools on or off.

Any MCP client that supports Streamable HTTP and OAuth sign-in can connect, such as Antigravity CLI.

Enter https://biohub.ai/mcp as the server URL, and choose Streamable HTTP, sometimes labeled HTTP, if the client asks.
Choose OAuth sign-in if the client asks, and leave any client ID and secret fields empty.
Do not select the older SSE transport, which cannot connect.

Show me the 3D structure of green fluorescent protein (GFP), colored by confidence, with its chromophore residues Ser65, Tyr66, and Gly67 highlighted. Look at the structure and tell me where the chromophore sits and how confident the prediction is.

Copy and paste the prompt above into your AI agent. Your AI agent finds GFP from Aequorea victoria in UniProt (P42212, 238 residues) with esm_atlas_search_uniprot, then shows its structure with ui_show_structure. If the ESM Atlas does not have a stored structure for a protein, it predicts one, which takes a little longer.You should see an 11-stranded beta barrel with a helix running through its center, which carries the three highlighted chromophore residues. The prediction’s pTM is about 0.91, and most residues are colored dark blue for high confidence. Agents that support MCP Apps display the structure in an interactive viewer you can rotate, while agents that do not will display a static image.This request is free. Folding, mutation scoring, and complexes are billed to your account, as the Folding tools and Mutation scoring tools pages show. If your AI agent does not find the Biohub tools, or still says you need to sign in, see Troubleshooting.

Biohub MCP

Tools

Skills

Security and support

Connect to the Biohub MCP and run your first query

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