How to Use the EBI InterPro MCP in Cline
Cline runs automated protein classification workflows using the EBI InterPro MCP Server.
Works with every AI agent you already use
…and any MCP-compatible client
Connect EBI InterPro MCP to Cline
Create your Vinkius account to connect EBI InterPro to Cline and route execution through our secure gateway. The platform manages server hosting, runtime updates, and security layers. Configuration requires no manual server provisioning.
End-to-end protein family classification
Cline uses `search_entries` to find relevant families based on your keywords. It then triggers `get_entry` to pull the full metadata, including Gene Ontology terms and literature counts. This allows you to automate the entire annotation process. Cline compiles the data into your project files, keeping your documentation accurate without manual copy-pasting.
Automated structural cross-referencing
When you need to verify a protein's structure, Cline executes `get_structure` with the target PDB ID. It maps the InterPro annotations onto the PDB data, giving you a complete view of the protein's functional sites. It handles the API calls and formats the output into readable reports. You define the sequence, and Cline builds the analysis.
Proteome-wide domain analysis
Give Cline a proteome ID, and it uses `get_proteome` to generate a summary of domain coverage. It processes the statistics for every protein associated with that organism. This tool is useful for batch-processing large datasets. Cline iterates through the results and flags proteins that match your specific functional criteria.
Set up EBI InterPro MCP in Cline
Prerequisites
- VS Code with Cline extension installed
- Active Vinkius subscription with a valid endpoint token
- 1
Open Cline MCP settings
Click the Cline icon in the VS Code sidebar to open the Cline panel. Then click the MCP Servers icon (server stack) at the top-right corner of the panel.
- 2
Add a remote server
Click "Remote Servers" at the top, then click "Add Remote MCP". In the Name field, type
ebi-interpro-mcp. In the URL field, paste your Vinkius endpoint:https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp. Get your token from cloud.vinkius.com. - 3
Enable the server
After saving, the server appears in the Cline MCP panel. Toggle the switch to enable it. The status indicator turns green when the connection is live.
- 4
Start using tools
Return to the Cline chat and ask: "Check my latest EBI InterPro refund status." Cline will discover the available tools and request your approval before invoking each one — giving you full control over every action.
{
"mcpServers": {
"ebi-interpro-mcp": {
"url": "https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp"
}
}
}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 Cline
Use it with your favorite AI tools
Connect this server to Cursor, Claude, VS Code, and more.
Start using the EBI InterPro MCP today
We host it, we monitor it, we maintain it. You just paste one token.
