• IDENTIFICATION
  • SITE MAPPING
  • DATA RETRIEVAL
  • HUMAN REVIEW

How to annotate protein functional domains with your AI

Connect your AI to InterPro to pull domain and family data directly from protein sequences. Your agent handles the database lookups while you focus on the biological implications.

Ask AI about this page

Short answer

How can I use AI to annotate protein domains?

Your AI queries the InterPro database to map protein sequences to specific families, domains, and functional sites. You get structured annotations and functional site identifications without manual database searching. This process maps your sequences to known biological signatures.

Annotation outcomes

What your AI produces

The specific data your agent pulls from InterPro.

IDENTIFICATION

Family and domain mapping

The AI identifies specific protein families and structural domains. You receive a clear list of biological classifications for your input.

SITE MAPPING

Functional site detection

Your agent finds specific functional sites within the sequence. This highlights active sites or binding regions identified by InterPro.

DATA RETRIEVAL

Protein entry details

The AI pulls full entry details for specific proteins. You get the context needed to understand the protein's role.

HUMAN REVIEW

Validation required

The AI provides the raw annotations from the database. You must verify these findings against your specific experimental context.

The workflow

What your AI does when a sequence arrives.

The AI moves from raw sequence to a complete functional profile using InterPro tools.

  1. Search for entries

    The AI searches the InterPro database to find relevant protein entries based on your sequence or identifiers.

    search_entries

  2. Retrieve protein data

    Once a match is found, the AI pulls the specific protein record to access its full domain profile.

    get_protein

  3. Fetch entry lists

    The AI gathers a list of all related protein entries to ensure the annotation is comprehensive.

    get_protein_entries

  4. Synthesize annotations

    The AI compiles the domain, family, and site information into a readable summary for your analysis.

    get_protein

Try it

Copy these to start.

Use these prompts to begin your annotation task.

Starting points

Replace the bracketed text with your actual protein accession numbers or sequences.

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

  • Search InterPro for the protein entry with accession P12345 and list its functional domains.

  • Identify the protein families associated with this sequence: [insert sequence].

  • Get the functional site details for the protein entry UniProt ID Q9H4A4.

  • Find all protein entries related to the domain 'Zinc finger' using InterPro.

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

Start here

Connect EBI InterPro once, then ask.

One connection gives your AI access to the full InterPro database. Your credentials stay encrypted and secure.

Connect EBI InterPro to your AI

FAQ

How the annotation task behaves

  • 01

    Can the AI predict new domains not in InterPro?

    No. The AI only retrieves and reports existing annotations found within the InterPro database.

  • 02

    Can the AI modify the protein records in the database?

    No. The AI can only read and query data; it cannot change or delete any entries in InterPro.

  • 03

    Does the AI provide structural models?

    No. It provides functional domain and family annotations based on the database entries.

  • 04

    Can I use this for custom sequence searches?

    Yes. You can provide a sequence to the AI to find matching entries in the database.

  • 05

    Will the AI automatically save these annotations to my files?

    No. The AI provides the information in the chat. You must manually save or export the results.

  • 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