Do I need an API key to use this MCP?

No, you can start searching molecular structures immediately after connecting without an API key.

What kind of structures can I find?

You can access over 220,000 experimentally determined 3D structures for proteins, DNA, and RNA.

Which AI clients can use this?

This MCP works with any compatible client, including Claude, Cursor, Windsurf, and VS Code.

Can I search by experimental method?

Yes, you can search for structures determined by X-ray, Cryo-EM, or NMR.

How do I identify a specific structure?

You can use the 4-character PDB ID, such as 1HHO, to get full structural details.

What experimental methods are represented in the PDB?

The PDB contains structures determined by four main methods: X-ray Crystallography (85% of entries, atomic resolution), Cryo-EM (rapidly growing, now 15%+ of new deposits), NMR Spectroscopy (solution-state structures), and Neutron Diffraction (hydrogen atom positions). Each entry lists its method and resolution.

Do I need authentication to access PDB data?

No. RCSB PDB is completely free and open. funded by NSF, NIH, DOE, and international partners. All 220K+ structures are openly accessible without any registration or API key. The data is licensed under CC0 (public domain).

What information does each PDB entry contain?

Each entry includes: PDB ID (4-character code), structure title, depositing authors, experimental method, resolution in Ångströms, source organism, release date, number of polymer chains, and bound non-polymer ligands (drugs, cofactors, ions). Higher resolution (lower number) means more precise atomic coordinates.

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Connect RCSB PDB to ChatGPT, Claude and Gemini

Set it up once and it works in ChatGPT, Claude, Cursor, and any other client you love. It all runs safely in the background, so you can relax and focus on what really matters. Access 220,000 experimental 3D structures through your AI agent.

Ask AI about this Connector

Developed, maintained, and hosted by Vinkius.

MCP VERIFIED · PRODUCTION READY · VINKIUS GUARANTEED

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Works with modern AI clients that support MCP, including ChatGPT, Claude, Cursor, and more.

Your AI does the work. We keep it safe and sound.

No other AI tool gives you this. Your workflow runs in the client you already love, your account stays protected, and you decide what the agent can and cannot do. It is the whole reason to make the switch.

Each Connector lives inside our infrastructure, the same place where your workflow runs. The three things below are already part of it, working quietly in the background so you never have to think about them. Nothing to add, nothing to set up, nothing to worry about.

V8 Isolate01

Each Connector runs inside its own sealed environment.

Each Connector runs inside its own sealed V8 runtime — no access to your files, your system, or other servers. A Connector never sees past its own request.

Kill Switch02

One switch stops every agent. Instantly.

One action deactivates every Connector, revokes every token, and ends every session at once. AI Governance keeps the record.

FinOps per User03

Spending limits that pause instead of surprise.

Every user keeps their own connections and credentials, isolated from everyone else. Anything that would cross your spending limit is held for your approval, not billed.

Three controls, built into the layer your AI connects through.

Curated set · 2 capabilities

We ship only the actions that matter.

Capability set01 / 01

01-02

2 capabilities in this set.

Part of 2 available through RCSB PDB.

01
Get pdb structure
Retrieves complete structural details for a specific 4-character PDB ID like 1HHO or 6LU7.
02
Search pdb
Searches the database of 220,000+ entries to return PDB IDs, titles, experimental methods, resolutions, and bound ligands.

Real work

What teams actually run

Target Identification

Search for protein structures associated with specific diseases to begin research.

Ligand Screening

Find co-crystal structures to identify how specific molecules bind to a target protein.

Method Comparison

Query different experimental methods like Cryo-EM or X-ray to compare structural resolutions.

Data Verification

Check the resolution and authorship of a specific PDB entry via your agent.

Automate a task

Put RCSB PDB to work on one thing.

Step-by-step automations your AI runs through this Connector: the workflow, the prompts to start with, and the exact capabilities behind each move.

One connector, every AI

RCSB PDB works with the most popular AI clients.

These are the most popular clients, each with a step-by-step guide: one link, set up once, with governance and visibility built in. And because everything runs on the MCP standard, the same connection also works in any other compatible client — nothing to rebuild.

Building your own app? The connector is yours to use.

You don't need a client to put RCSB PDB to work: the same hosted connection plugs into your own applications and agent code, with the same governance on every request. Build with it, chat with it — one connection for both.

Observed, not estimated

907ms average. Fast in production.

RCSB PDB is checked daily against the live service.

Daily averagePeak 1080ms

Oct 3Today

Fastest day: 730ms
Slowest day: 1080ms
14-day trend: Slowing+19%

Connect your client

One URL. Every client.

Activate the Connector, copy your link, and paste it into the client you already use. 2 capabilities arrive ready to run.

Preview access · not provider authentication

The vk_preview_* token belongs to Vinkius preview infrastructure. It lets Claude discover and display the capabilities of RCSB PDB, so you can see the experience inside your AI.

It does not authenticate your account with RCSB PDB. Actions requiring credentials or live account data may not run until you activate the Connector and authorize the service.

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.

1In Claude Desktop, open Settings → Connectors.
2Click “Add custom connector” and paste the connector link above as the remote MCP server URL.
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"
    }
  }
}

Claude
ChatGPT
Cursor
VS Code
Windsurf
Claude Code
JetBrains
Cline

Step-by-step instructions for each client are in the guide. How to connect

Guided setup for Claude? Set up RCSB PDB in Claude and other AIs

See all the AI clients this connector works with ↑

Who it's for

Built for the work RCSB PDB owners hand off.

This MCP is designed for professionals working with biological macromolecules and structural data.

01
Structural Biologists
They use the agent to quickly pull experimental metadata and resolution details.
02
Drug Discovery Teams
They find protein-ligand co-crystal structures for virtual screening and design.
03
Biochemistry Students
They explore protein architecture using real experimental structures and annotations.

FAQ

Questions RCSB PDB owners ask.

01
Do I need an API key to use this MCP?
No, you can start searching molecular structures immediately after connecting without an API key.
02
What kind of structures can I find?
You can access over 220,000 experimentally determined 3D structures for proteins, DNA, and RNA.
03
Which AI clients can use this?
This MCP works with any compatible client, including Claude, Cursor, Windsurf, and VS Code.
04
Can I search by experimental method?
Yes, you can search for structures determined by X-ray, Cryo-EM, or NMR.
05
How do I identify a specific structure?
You can use the 4-character PDB ID, such as 1HHO, to get full structural details.
06
What experimental methods are represented in the PDB?
The PDB contains structures determined by four main methods: X-ray Crystallography (85% of entries, atomic resolution), Cryo-EM (rapidly growing, now 15%+ of new deposits), NMR Spectroscopy (solution-state structures), and Neutron Diffraction (hydrogen atom positions). Each entry lists its method and resolution.
07
Do I need authentication to access PDB data?
No. RCSB PDB is completely free and open. funded by NSF, NIH, DOE, and international partners. All 220K+ structures are openly accessible without any registration or API key. The data is licensed under CC0 (public domain).
08
What information does each PDB entry contain?
Each entry includes: PDB ID (4-character code), structure title, depositing authors, experimental method, resolution in Ångströms, source organism, release date, number of polymer chains, and bound non-polymer ligands (drugs, cofactors, ions). Higher resolution (lower number) means more precise atomic coordinates.

Explore

More in The Unthinkable

Connect RCSB PDB to Claude, Cursor, ChatGPT & more

Your AI does the work. We keep it safe and sound.

Each Connector runs inside its own sealed environment.

One switch stops every agent. Instantly.

Spending limits that pause instead of surprise.

We ship only the actions that matter.

01-02

Get pdb structure

Search pdb

What teams actually run

Target Identification

Ligand Screening

Method Comparison

Data Verification

Building your own app? The connector is yours to use.

RCSB PDB Connector

Claude Desktop

Structural Biologists

Drug Discovery Teams

Biochemistry Students

Do I need an API key to use this MCP?

What kind of structures can I find?

Which AI clients can use this?

Can I search by experimental method?

How do I identify a specific structure?

What experimental methods are represented in the PDB?

Do I need authentication to access PDB data?

What information does each PDB entry contain?

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