• IDENTIFIERS
  • METADATA
  • FILTERING
  • HUMAN

How to search protein structures with your AI

Connect your agent to the RCSB PDB database to pull structural data using natural language.

Ask AI about this page

Short answer

How can I find protein structures with my AI?

Your agent uses the search_pdb tool to query the RCSB PDB database for entries matching your biological criteria. You'll get direct PDB IDs based on organism, disease, or function. This breakdown shows what you get.

Search outcomes

What you get from a query

The specific data points your agent returns.

IDENTIFIERS

Direct PDB IDs

The AI finds the exact PDB entry IDs that match your biological query. You get the specific codes needed for your research.

METADATA

Biological context

The agent pulls relevant metadata like organism type or functional descriptions. This helps you confirm the structure is the right one.

FILTERING

Targeted results

The search narrows down thousands of entries to a specific subset. You avoid manual filtering through the web interface.

HUMAN

Manual verification

You must review the returned PDB IDs to ensure they meet your specific experimental or resolution requirements. The AI provides the data, but you make the final selection.

The workflow

What your AI does when a search request arrives.

The agent translates your biological questions into database queries.

  1. Interpret intent

    Your agent parses your request to identify the target organism, disease, or protein function you are looking for.

    search_pdb

  2. Query the database

    The agent uses the search tool to scan the RCSB PDB for matching structural entries.

    search_pdb

  3. Filter results

    The agent organizes the returned PDB entries to match your specific constraints.

    search_pdb

  4. Present data

    The agent provides you with a list of PDB IDs and their associated biological information.

    search_pdb

Try it

Copy these to start.

Use these prompts to begin your search.

Starting points

Swap out the bracketed terms for your specific research targets.

RCSB PDB Connector

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

Connector linkhttps://edge.vinkius.com/vk_preview_px4KJXLkPAfRiw8dj06D8ILeCL0RIsHNqISA0zQD/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 — RCSB PDB capabilities are ready to use.
Configuration · claude_desktop_config.jsonCopy
{
  "mcpServers": {
    "rcsb-pdb-mcp": {
      "url": "https://edge.vinkius.com/vk_preview_px4KJXLkPAfRiw8dj06D8ILeCL0RIsHNqISA0zQD/mcp"
    }
  }
}
Copy into chat04

  • Find PDB entries for proteins associated with Alzheimer's disease.

  • Search for protein structures in Homo sapiens related to insulin signaling.

  • List PDB IDs for structures involving hemoglobin in humans.

  • Find all structures related to DNA polymerase in E. coli.

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

Start here

Connect RCSB PDB once, then ask.

One click connects the database to your agent. Your credentials stay encrypted, and you can start querying immediately.

Connect RCSB PDB to your AI

FAQ

How the search behaves

  • 01

    Can the AI download the actual PDB files?

    No. The agent uses the search tool to find PDB IDs and metadata, but it does not download or provide the raw coordinate files.

  • 02

    Can I ask for structures with a specific resolution?

    No. The current search tool focuses on biological function, organism, and disease associations. It does not filter by experimental resolution.

  • 03

    Does the AI update the database?

    No. The agent only reads data from the RCSB PDB. It cannot add, edit, or delete any entries in the database.

  • 04

    Can I use this to find proteins in any organism?

    Yes, as long as the organism is represented in the RCSB PDB database.

  • 05

    Will the AI suggest new proteins?

    No. The agent only searches for existing entries that are already documented in the RCSB PDB.

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

Connect RCSB PDB to Claude, Cursor, ChatGPT & more