Connect to Biohub MCP and run your first query

This quickstart connects Biohub MCP to your AI client, checks that its seven tools are available, and runs one request with a known answer. You don’t need a Biohub account or an API key.

Before you begin

You need an MCP client that can connect to a remote Streamable HTTP server, such as Codex, Claude, ChatGPT, or Cursor. Some clients limit custom servers by plan or by admin setting. Connect your client lists those requirements.

Add Biohub MCP to your client

Codex
Claude Code
Claude.ai / Claude Desktop
ChatGPT
Cursor

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

Run codex mcp list to check it. The auth column reads Unsupported, which is expected because the server has no sign-in. Start a new codex session to use it.The same entry works in the ChatGPT desktop app and the Codex IDE extension. To add it from the desktop app instead, see Connect your client.

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

Run claude mcp list to check it. Start a new claude session to use it, and enter /mcp there to see the server.

Open Customize, then Connectors.
Click +, then Add custom connector.
Enter https://biohub.ai/mcp as the remote MCP server URL and Biohub as the name, leave Advanced settings empty, and click Add.
In a chat, click +, choose Connectors, and turn on Biohub.

Developer mode is available on the web for Plus, Pro, Business, Enterprise, and Education accounts.

In ChatGPT on the web, open Settings, then Security and login, and turn on Developer mode.
Open chatgpt.com/plugins and select + 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, choose No Authentication, and create it.
In a chat, choose Developer mode from the + menu and select Biohub.

Add this entry to ~/.cursor/mcp.json, keeping any servers already listed there:

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

Check it in Cursor’s MCP settings.

Confirm the tools

List the Biohub MCP tools you can use, without calling any of them.

You should see these seven tools, possibly with a prefix such as mcp__biohub__:

esm_atlas_search_uniprot
esm_atlas_lookup_accession
esm_atlas_get_protein_details
esm_atlas_search_similar_protein_clusters
esm_atlas_get_cluster_info
esm_atlas_get_sae_feature_detail
ui_show_protein_structure

If tools are missing, see Troubleshooting.

Run a first request

Use Biohub to look up UniProt accession P42212. Tell me the protein name, organism, gene, and sequence length. Don't print the full sequence.

The assistant calls esm_atlas_search_uniprot and should report Green fluorescent protein (gene GFP) from Aequorea victoria, 238 residues long. That matches the UniProt record for P42212.

Next steps

Ask for proteins similar to GFP, or view a structure, with the Example prompts.
Set up another client with Connect your client.
Learn what the tools accept and return in the ESM Atlas tools reference.

​Before you begin

​Next steps

Before you begin

Next steps