How to Use the EBI InterPro MCP in Windsurf

Cascade chains these 16 tools to map protein domains directly within Windsurf.

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Connect EBI InterPro MCP to Windsurf

Create your Vinkius account to connect EBI InterPro to Windsurf and route execution through our secure gateway. The platform manages server hosting, runtime updates, and security layers. Configuration requires no manual server provisioning.

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Setup EBI InterPro with Windsurf

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Claude

Perplexity

Autonomous protein domain discovery

Cascade reads your codebase and calls `search_proteins` to identify relevant sequences without your intervention. It then links these to specific functional data using `get_protein_entries` to map out the domain architecture. Once the domains are identified, your agent automatically fetches the taxonomic background via `get_entry_taxonomy`. This allows you to see how a specific protein family has evolved across different organisms in a single pass.

Structural data integration for Windsurf

You can tell Cascade to reconcile 1D sequence data with 3D structural reality using `get_entry_structures`. It pulls PDB IDs and experimental resolutions to confirm if the predicted domain actually holds up in a physical model. This MCP Server provides the raw data, and Cascade handles the cross-referencing. It saves you from manually jumping between browser tabs to verify if a sequence fold is supported by recent experimental data.

Taxonomic lineage mapping

Use `search_taxonomy` to verify organism data before running deep analysis on protein families. It clears up ambiguity by providing exact lineage and protein counts for the species you are investigating. Cascade uses `get_taxonomy` to pull the full hierarchy, ensuring your functional annotations are grounded in the correct biological context. It turns a complex database search into a background task.

Setup guide

Set up EBI InterPro MCP in Windsurf

Prerequisites

Windsurf IDE installed (macOS, Windows, or Linux)
Active Vinkius subscription with a valid endpoint token

1

Open MCP configuration

Click the Cascade assistant icon in the sidebar, then click the hammer icon (🔨) at the top of the panel. Select "Configure" to open ~/.codeium/windsurf/mcp_config.json.
2

Add the EBI InterPro MCP

Paste the JSON snippet shown on the right into the mcpServers object. Replace [YOUR_TOKEN_HERE] with your endpoint token from cloud.vinkius.com.
3

Refresh MCPs

Go back to the hammer icon (🔨) in Cascade and click "Refresh". Windsurf will detect the new server. No full restart is needed — the connection is hot-reloaded.
4

Verify in Cascade

Start a new Cascade conversation and ask something like "Show my EBI InterPro payment history." If connected, Cascade will call the EBI InterPro tools directly. You will see a green dot next to the server name in the MCP panel.

mcp_config.json

{
  "mcpServers": {
    "ebi-interpro-mcp": {
      "url": "https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp"
    }
  }
}

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Common questions about EBI InterPro MCP in Windsurf

Open your chat panel and ask Cascade to search for a protein by name. It uses the `search_proteins` tool to query the EBI InterPro database directly from your current workspace.

Yes. Just provide the Pfam accession, and Cascade will invoke `get_pfam_entry` to return the domain details immediately. It eliminates the need to leave your editor.

No. The server requires a live connection to the EBI API endpoints to fetch current classification data. You need internet access for these tools to return results.

The server reports exactly what the database provides. If the accession is invalid or the protein has no known domains, the tool returns an empty set so you know to refine your query.

Your queries stay between your Windsurf instance and the EBI API. This MCP Server does not store your protein sequences or track your research history on any external servers.

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