• DATA
  • MAPPING
  • FILTER
  • HUMAN

How to find protein structural models with your AI

Connect EBI InterPro to your agent to bridge the gap between functional domain definitions and 3D structural data.

Ask AI about this page

Short answer

How can I find protein structural models using my AI?

You ask your AI for structures associated with a specific InterPro entry or domain. It uses the EBI InterPro connector to fetch relevant PDB IDs and structural data. You get a list of specific models ready for your analysis.

The results

What you get from this task

The AI handles the data retrieval so you can focus on the biology.

DATA

Direct PDB links

The AI finds specific PDB identifiers that match your domain requirements. You get the exact IDs needed for structural viewing.

MAPPING

Domain to structure

It maps InterPro functional descriptions to physical 3D models. This connects what a protein does to how it looks.

FILTER

Targeted search

Instead of browsing manually, your agent narrows down structures to only those representing the specific functional site you care about.

HUMAN

Expert review

The AI provides the data, but you must decide which specific model is high-enough resolution or relevant enough for your study.

The workflow

What your AI does when the request arrives.

The AI moves from functional definitions to specific structural coordinates.

  1. Identify the entry

    Your agent identifies the correct InterPro entry or domain based on your description.

    get_entry_structures

  2. Fetch structure list

    The AI pulls a list of all PDB structures associated with that specific functional entry.

    get_entry_structures

  3. Select specific model

    Once you pick a target, the AI retrieves the detailed information for that individual structure.

    get_structure

  4. Present findings

    The AI delivers the PDB IDs and relevant metadata to your chat interface.

    get_structure

Try it

Copy these to start.

Use these prompts to trigger the EBI InterPro tools.

Starting points

Swap out the InterPro IDs or domain names for the ones you are actually researching.

InterPro Connector

You're all set. Choose your MCP client and follow the setup instructions.

Connector linkhttps://edge.vinkius.com/vk_preview_cBrAY2Gy2NSFguudqzcAnkyhKLGxzkfF44ThKH5h/mcp

Claude Desktop

Follow the steps below to connect in seconds.

  1. 1In Claude Desktop, open Settings → Connectors.
  2. 2Click “Add custom connector” and paste the connector link above as the remote MCP server URL.
  3. 3Click Add and start a new chat — InterPro capabilities are ready to use.
Configuration · claude_desktop_config.jsonCopy
{
  "mcpServers": {
    "ebi-interpro-mcp": {
      "url": "https://edge.vinkius.com/vk_preview_cBrAY2Gy2NSFguudqzcAnkyhKLGxzkfF44ThKH5h/mcp"
    }
  }
}
Copy into chat04

  • Find all PDB structures associated with InterPro entry IPR001234.

  • Get the structural models for the domain described in InterPro entry IPR005678.

  • List the PDB IDs for structures that represent the functional site in IPR009999.

  • Show me the details for the PDB structure 1ABC that is linked to this InterPro entry.

  • Claude
  • ChatGPT
  • Cursor
  • VS Code
  • Windsurf
  • Claude Code
  • JetBrains
  • Cline

Start here

Connect EBI InterPro once, then ask.

One click connects the MCP to your client. Your credentials stay encrypted and you can start querying immediately.

Connect EBI InterPro to your AI

FAQ

How this task behaves

  • 01

    Can the AI download the actual PDB files?

    No. The AI retrieves the structural data and PDB identifiers, but you must download the files through your own structural biology software.

  • 02

    Can the AI edit InterPro entries?

    No. The AI can only read data from EBI InterPro to find structures. It cannot modify the database.

  • 03

    Does it work with any protein ID?

    It works with any valid InterPro entry or domain ID that has associated structural data in the database.

  • 04

    Can the AI perform structural alignment?

    No. The AI finds the models for you, but the actual alignment or docking work stays with you and your specialized tools.

  • 05

    How does it find the structures?

    It uses the get_entry_structures tool to find all models mapped to a specific InterPro entry.

  • More questions about EBI InterPro? The Connector page answers them. See everything the EBI InterPro Connector can do

Connect InterPro to Claude, Cursor, ChatGPT & more