How to Use the EBI InterPro MCP in VS Code Copilot

Q: How does our team share the EBI InterPro configuration in VS Code Copilot?

You commit a .vscode/mcp.json file to your Git repository. This lets every team member access the same MCP server tools, like getprotein and getstructure, without individual setup.

Q: Can VS Code Copilot help us map PDB structures using EBI InterPro?

Yes, Copilot queries getentrystructures to find physical representatives for any InterPro family. It then uses getstructure to overlay domain annotations onto those PDB records right in your workspace.

Q: Does VS Code Copilot support the Conserved Domain Database from EBI InterPro?

Yes, Copilot can query CDD entries directly. It uses getcddentry to fetch curated models and alignments, helping your team build precise functional annotation pipelines.

Share standardized EBI InterPro workflows and query protein databases across your engineering team in VS Code Copilot via MCP.

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Connect EBI InterPro MCP to VS Code Copilot

Create your Vinkius account to connect EBI InterPro to VS Code Copilot 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 VS Code Copilot

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Standardize Biological Queries across Teams

`get_entry` pulls standard family, domain, and homologous superfamily metadata directly into your shared VS Code Copilot workspace. By configuring this tool team-wide, every developer can access consistent annotations for accessions like IPR036291. This eliminates discrepancies where team members use outdated local database files. VS Code Copilot reads live data using `list_entry_databases` to ensure everyone is querying the exact same database versions.

Automate Taxonomic Mapping with this MCP Server

`get_entry_taxonomy` extracts taxonomic distributions directly into your VS Code Copilot chat window. Your team can quickly verify which organisms express a specific domain during collaborative debugging sessions. The tool queries taxonomy nodes and ranks, which VS Code Copilot then formats into markdown tables. You can also run `search_taxonomy` to verify specific organism IDs like 9606 for human targets.

Map Proteomes in VS Code Copilot

`get_proteome` retrieves domain coverage statistics for entire reference proteomes directly into your active project. When your team is building comparative genomics tools, Copilot uses this data to write precise validation tests. It queries UniProt proteome IDs and returns associated entry counts. VS Code Copilot then uses `get_entry_proteins` to verify that your code correctly maps proteins to their respective families.

Setup guide

Set up EBI InterPro MCP in VS Code Copilot

Prerequisites

VS Code 1.99 or later with GitHub Copilot extension
Active Vinkius subscription with a valid endpoint token

1

Open MCP configuration

Open the Command Palette (Cmd+Shift+P / Ctrl+Shift+P) and run "MCP: Add Server". Select HTTP (Streamable) as the server type. VS Code will create .vscode/mcp.json in your workspace.
2

Add the EBI InterPro MCP

Paste the JSON snippet shown on the right into your .vscode/mcp.json. Replace [YOUR_TOKEN_HERE] with your endpoint token from cloud.vinkius.com.
3

Switch to Agent mode

Open Copilot Chat (Cmd+Shift+I / Ctrl+Shift+I) and switch to Agent mode using the dropdown. MCP tools are only available in Agent mode — they do not appear in Edit or Ask modes.
4

Verify the connection

In the Copilot Chat input, type # to list available tools. You should see the EBI InterPro tools listed. Try asking: "List my recent EBI InterPro transactions" and Copilot will invoke them automatically.

.vscode/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 VS Code Copilot

You commit a `.vscode/mcp.json` file to your Git repository. This lets every team member access the same MCP server tools, like `get_protein` and `get_structure`, without individual setup.

Yes, Copilot queries `get_entry_structures` to find physical representatives for any InterPro family. It then uses `get_structure` to overlay domain annotations onto those PDB records right in your workspace.

Ask Copilot to find entries matching a keyword like kinase. The agent calls `search_entries` to pull accessions, names, and protein counts, allowing your team to quickly select the correct target.

Yes, Copilot can query CDD entries directly. It uses `get_cdd_entry` to fetch curated models and alignments, helping your team build precise functional annotation pipelines.

The MCP server runs in an isolated V8 sandbox on Vinkius, ensuring your sequence queries and taxonomy lookups are handled ephemerally. No biological data is stored, and all communication with the EBI API is fully encrypted.

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