How to Use the EBI InterPro MCP in Claude

Q: How does Claude Desktop handle database cross-references from EBI InterPro?

The desktop app uses listentrydatabases to see which member databases are active. Then, when you query an entry via getentry, Claude Desktop maps the cross-references to Pfam, CDD, or PANTHER automatically.

Parse protein sequences and map domains directly inside your Claude Desktop chat using this MCP server.

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Connect EBI InterPro MCP to Claude Desktop

Create your Vinkius account to connect EBI InterPro to Claude Desktop 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 Claude Desktop

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Map Protein Domains in Chat

`get_protein_entries` is the tool that queries the InterPro database to identify domains within your specific protein. You paste a UniProt accession or sequence name into Claude Desktop, and the server retrieves the exact family assignments, domain boundaries, and functional sites. This stops you from jumping back and forth to the EBI web portal during your analysis. Claude Desktop uses `get_protein` and `get_pfam_entry` to build a complete profile of your target protein, showing you exactly where active sites sit without leaving your chat window.

Trace Evolutionary Lineages with Claude Desktop

`get_entry_taxonomy` maps the distribution of a protein family across the tree of life. When you ask Claude Desktop to analyze an evolutionary path, it queries the node counts and ranks to show you which organisms share the domain. You can then use `get_taxonomy` and `get_proteome` to compare domain coverage statistics between model organisms. The desktop client displays these taxonomic trees directly in your chat history, making evolutionary profiling a simple conversational task.

Pull Structural Data with this MCP Server

`get_entry_structures` fetches physical 3D coordinates and experimental resolutions for any InterPro entry. Your AI client calls this MCP tool to find high-resolution PDB representatives for the protein family you are investigating. Once you find a candidate, `get_structure` pulls the mapped annotations for that specific PDB ID. Claude Desktop digests the structural details and highlights key residues, saving you from manual PyMOL lookups.

Setup guide

Set up EBI InterPro MCP in Claude Web or Desktop

1

Open Claude Settings

Go to claude.ai, click your profile icon, then navigate to Customize → Connectors.
2

Add Custom Connector

Click the "+" button and select Add custom connector. Paste your Vinkius endpoint URL: https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp Replace [YOUR_TOKEN_HERE] with your token from cloud.vinkius.com. For OAuth-protected servers, expand Advanced settings to add credentials.
3

Start a conversation

Open a new chat. The EBI InterPro MCP tools are available immediately — no restart needed.

Endpoint URL

https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp

No configuration file needed — paste the URL directly in the Claude web interface.

Available on Free (1 connector), Pro, Max, Team, and Enterprise plans.

Prerequisites

Claude Desktop installed (macOS or Windows)
Active Vinkius subscription with a valid endpoint token

1

Open Claude Desktop Settings

Click the menu icon at the top-left corner, go to Settings → Developer → Edit Config. This opens claude_desktop_config.json in your default text editor.
2

Paste the EBI InterPro MCP configuration

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

Restart Claude Desktop

Close and reopen the application. Claude needs a full restart to load new MCPs — refreshing a conversation is not enough.
4

Verify the connection

Open a new conversation. Click the 🔌 icon at the bottom of the message input. You should see tools listed under ebi-interpro-mcp.

json

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

Get your connection token →

Independent Platform Disclaimer: Vinkius is an independent platform and is not affiliated with, endorsed by, sponsored by, verified by, or otherwise authorized by InterPro. All third-party trademarks, logos, and brand names are the property of their respective owners. Their use on this website is strictly for informational purposes to identify service compatibility and interoperability.

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Common questions about EBI InterPro MCP in Claude Desktop

Use the chat input to ask Claude Desktop to find a domain, which triggers `search_entries` under the hood. The server queries the database and returns matching accessions, allowing you to immediately call `get_pfam_entry` for deeper structural details.

Yes, you can check proteome-wide domain coverage by asking the desktop client to query a UniProt proteome ID. It invokes `get_proteome` to pull down the entire organism profile and summarizes the dominant protein families for you.

The desktop app uses `list_entry_databases` to see which member databases are active. Then, when you query an entry via `get_entry`, Claude Desktop maps the cross-references to Pfam, CDD, or PANTHER automatically.

No code is required because this MCP server exposes raw database lookups as simple conversational actions. You just ask Claude Desktop about a protein like insulin, and it runs `search_proteins` and `get_protein` behind the scenes.

Your queries, sequence accessions, and PDB IDs go directly to the secure Vinkius MCP gateway, which communicates with the public EBI API. No sequence data or search terms are ever cached or used to train models.

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