• DOMAIN
  • PTM
  • SITE
  • HUMAN

How to analyze protein functional features with your AI

Connect the EBI Proteins API to your AI client to pull specific biological data from the EBI database.

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Short answer

How can I use my AI to analyze protein functional features?

Your AI queries the EBI Proteins API to find specific domains, binding sites, and PTMs. You get structured functional data instead of hunting through raw databases. This allows you to map specific protein characteristics directly in your chat.

Data outcomes

What your AI extracts

The specific biological data your agent pulls from EBI.

DOMAIN

Protein domain maps

The AI identifies functional domains within a sequence. You get a list of structural units and their roles.

PTM

Modification profiles

Your agent retrieves post-translational modification data. This shows where a protein is modified after synthesis.

SITE

Binding site locations

The AI finds specific binding and functional sites. You can use this to pinpoint interaction points.

HUMAN

Manual interpretation

The AI provides the raw data and summaries. You must perform the final biological analysis and experimental design.

The workflow

What your AI does when the request arrives.

The AI acts as a bridge between your questions and the EBI database.

  1. Filter feature types

    The AI looks up available feature categories to understand what data is accessible for a specific protein.

    search_features_by_type

  2. Fetch domain data

    The agent pulls specific structural and functional domain information for the target protein.

    get_protein_features

  3. Retrieve PTMs

    The AI queries the database for specific post-translational modifications associated with the protein.

    get_proteomics_ptm

  4. Summarize features

    The AI combines the domain and modification data into a single functional summary for your review.

    get_protein_features

Try it

Copy these to start.

Use these prompts to begin your analysis.

Starting points

Swap out the protein IDs and feature types for your specific research targets.

EMBL-EBI Proteins API Connector

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

Connector linkhttps://edge.vinkius.com/vk_preview_3jKiKjDDYj38o3vJ2cr3PVaRBrqDRzHtZH05tPSn/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 — EMBL-EBI Proteins API capabilities are ready to use.
Configuration · claude_desktop_config.jsonCopy
{
  "mcpServers": {
    "ebi-proteins-api-mcp": {
      "url": "https://edge.vinkius.com/vk_preview_3jKiKjDDYj38o3vJ2cr3PVaRBrqDRzHtZH05tPSn/mcp"
    }
  }
}
Copy into chat04

  • Find all the functional domains for the protein P12345.

  • List the post-translational modifications for the human insulin protein.

  • Search for all binding site features available in the EBI database.

  • Analyze the protein UniProt ID Q05653 and summarize its functional sites.

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

Start here

Connect EBI Proteins API once, then ask.

One click connects the API to your client. Your credentials stay encrypted and the setup is handled on our end.

Connect EBI Proteins API to your AI

FAQ

How this task behaves

  • 01

    Can the AI modify the protein data in the EBI database?

    No. The AI can only read and interpret data from the EBI Proteins API. It cannot write or change any biological records.

  • 02

    Does the AI perform the actual wet lab experiments?

    No. The AI only retrieves and summarizes existing computational and experimental data from the database.

  • 03

    Can I search for features by a specific type?

    Yes, the AI can use the search tool to find specific feature categories.

  • 04

    Will the AI automatically generate a lab report?

    No. The AI provides the data and summaries, but you must write and verify the final report.

  • 05

    Can the AI find PTM data for any protein?

    The AI can only find PTM data that is currently recorded in the EBI database.

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

Connect EMBL-EBI Proteins API to Claude, Cursor, ChatGPT & more