How to Use the EBI InterPro MCP in Claude Code

Q: How can I verify the EBI InterPro tools in Claude Code?

Run the command claude mcp list after adding the server. This confirms the connection and shows all registered tools available for your terminal session.

Q: Can I use EBI InterPro to query Pfam clans in Claude Code?

Yes. Use the getclan tool with a Pfam clan accession. Claude Code will output the member counts and description directly to your console.

Run EBI InterPro queries from your terminal with Claude Code.

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Connect EBI InterPro MCP to Claude Code

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

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Claude

Perplexity

Headless protein data retrieval

Pipe the output of `search_proteins` directly into your shell scripts for automated processing. It allows you to build CI/CD pipelines that validate protein annotations against the latest EBI data. Claude Code executes the tool call and returns the structured response to your terminal. You can parse the JSON output instantly.

Batch processing of entry databases

Use `list_entry_databases` to check the current scale of the InterPro member databases. This is useful for monitoring the data coverage of your automated pipelines. It provides a quick count of entries across different sources. You can integrate this into your build logs to track versioning or database updates.

Scripted taxonomy lookups

Automate your taxonomic filtering by calling `get_taxonomy` within your terminal workflow. It returns the lineage and protein counts for any organism ID you specify. This keeps your research scripts lean and direct. You avoid the overhead of a GUI by keeping the analysis inside your terminal sessions.

Setup guide

Set up EBI InterPro MCP in Claude Code

Prerequisites

Claude Code CLI installed (npm install -g @anthropic-ai/claude-code)
Active Vinkius subscription with a valid endpoint token

1

Run the add command

Open your terminal and run the command shown on the right. Replace [YOUR_TOKEN_HERE] with your endpoint token from cloud.vinkius.com. Use --scope user to make it available across all projects.
2

Verify the connection

Start a Claude Code session and type /mcp to list connected servers. You should see ebi-interpro-mcp with a green status indicator.
3

Start using tools

Ask Claude Code something like "Check my latest EBI InterPro transactions." It will automatically discover and invoke the available EBI InterPro tools.

Terminal

claude mcp add --transport http ebi-interpro-mcp https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp

Get your connection token →

Prerequisites

Claude Code CLI installed
Active Vinkius subscription with a valid endpoint token

1

Open the config file

Create or edit .mcp.json in your project root for project-level scope, or ~/.claude.json for user-level scope.
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

Restart Claude Code

Start a new Claude Code session. Type /mcp to confirm the server is connected. The tools will be automatically available in your conversation.

.mcp.json

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

Get your connection token →

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Common questions about EBI InterPro MCP in Claude Code

Run the command `claude mcp list` after adding the server. This confirms the connection and shows all registered tools available for your terminal session.

Yes. Use the `get_clan` tool with a Pfam clan accession. Claude Code will output the member counts and description directly to your console.

Yes, it supports standard HTTP and SSE transports. Configure your `~/.claude.json` file to point to the server endpoint for persistent access.

The server respects EBI API defaults. If you are running high-volume batch scripts, implement a basic wait or retry logic in your shell script to avoid hitting limits.

The server operates as a stateless proxy. It fetches biological data from the EBI database and transmits it to your terminal; no data is cached or stored by the server itself.

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