How to Use the EBI InterPro MCP in Cursor

Q: Does Cursor support bulk protein searches with EBI InterPro?

Cursor can loop through a list of accessions by calling searchproteins for each item. This server handles the rate limits, allowing the editor to build a structured JSON list of matching proteins inside your workspace.

Q: How do I configure Cursor to use the EBI InterPro tools?

Add the server configuration to your .cursor/mcp.json file in your project root. Once saved, Cursor immediately recognizes all 16 MCP tools, including getentry and gettaxonomy, in Agent mode.

Generate functional bioinformatics code in Cursor using live EBI InterPro structural and sequence data from our MCP server.

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Connect EBI InterPro MCP to Cursor

Create your Vinkius account to connect EBI InterPro to Cursor 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 Cursor

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Write Code with Live EBI InterPro Context

`get_protein` retrieves detailed protein profiles directly into your active Cursor coding session. When you are writing a script to parse sequence data, the editor calls this tool to inject real protein lengths, source organisms, and domain counts. This means you write code against actual biological data structures instead of guessing the JSON shape. Cursor uses `get_protein_entries` to verify your parsing logic against live UniProt records as you type.

Build Structural Pipelines in Cursor

`get_structure` maps InterPro annotations directly to 3D coordinates inside your Cursor workspace. If you are developing a structural biology pipeline, the editor uses this tool to fetch mapped PDB annotations without manual file downloads. You can chain this with `get_entry_structures` to automate the discovery of high-resolution structures for a given family. Cursor writes the retrieval loops for you, testing the code against live EBI endpoints in real time.

Query Pfam and CDD via Cursor's MCP Server

`get_pfam_entry` pulls domain-specific metadata directly into your workspace files. When you need to cross-reference Pfam domains with CDD models, Cursor invokes `get_cdd_entry` to compare alignments and functional sites. This integration turns your editor into a bioinformatic workbench. The MCP server handles the API queries, letting Cursor focus on generating clean, type-safe code for your sequence analysis.

Setup guide

Set up EBI InterPro MCP in Cursor

Prerequisites

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

1

Open MCP Settings

Go to Cursor Settings → MCP or open the Command Palette (Cmd+Shift+P / Ctrl+Shift+P) and search for "MCP: Add Server".
2

Add the EBI InterPro MCP

Cursor will create or open .cursor/mcp.json in your project root. Paste the JSON snippet on the right. Replace [YOUR_TOKEN_HERE] with your endpoint token from cloud.vinkius.com.
3

Enable Agent mode

Open Composer (Cmd+I / Ctrl+I) and switch to Agent mode using the dropdown at the top. MCP tools are only available in Agent mode.
4

Verify the connection

Ask Cursor something like "List my recent EBI InterPro transactions." If the MCP tools are loaded correctly, Cursor will call the EBI InterPro tools automatically. You can also check Settings → MCP for a green status indicator.

.cursor/mcp.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 Cursor

Yes, you can ask Cursor to write a script while referencing live data. The editor uses `get_protein` to verify the dictionary keys of the API response, ensuring your generated code runs without key errors.

Ask the Cursor agent to look up a clan accession like CL0001. The editor calls `get_clan` to retrieve the member counts and description, then inserts these details directly into your code comments or active file.

Cursor can loop through a list of accessions by calling `search_proteins` for each item. This server handles the rate limits, allowing the editor to build a structured JSON list of matching proteins inside your workspace.

Add the server configuration to your `.cursor/mcp.json` file in your project root. Once saved, Cursor immediately recognizes all 16 MCP tools, including `get_entry` and `get_taxonomy`, in Agent mode.

Yes, your local sequence files and proprietary accessions remain completely on your machine. The MCP server only sends the specific accession IDs or query strings you explicitly request to the EBI API via Vinkius's secure, ephemeral sandbox.

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