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.

RCSB PDB MCP Server for Windsurf 2 tools — connect in under 2 minutes

Name: RCSB PDB
Availability: InStock
Author: Vinkius

docs.windsurf.com/windsurf/mcp

Built by Vinkius GDPR 2 Tools IDE

Windsurf brings agentic AI coding to a purpose-built IDE. Connect RCSB PDB through Vinkius and Cascade will auto-discover every tool. ask questions, generate code, and act on live data without leaving your editor.

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Classic Setup·json

{
  "mcpServers": {
    "rcsb-pdb": {
      "url": "https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp"
    }
  }
}

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About RCSB PDB MCP Server

Connect your AI agent to the RCSB Protein Data Bank — the world's repository of experimentally determined 3D structural data for biological macromolecules.

Windsurf's Cascade agent chains multiple RCSB PDB tool calls autonomously. query data, analyze results, and generate code in a single agentic session. Paste Vinkius Edge URL, reload, and all 2 tools are immediately available. Real-time tool feedback appears inline, so you see API responses directly in your editor.

What you can do

Structure Search — Find protein, DNA, and RNA structures by name, function, disease association, or organism across 220K+ experimentally determined entries
PDB Entry Lookup — Get complete structural details by 4-character PDB ID (e.g., 1HHO for hemoglobin, 6LU7 for SARS-CoV-2 main protease) including experimental method, resolution, and bound molecules

The RCSB PDB MCP Server exposes 2 tools through the Vinkius. Connect it to Windsurf in under two minutes — no API keys to rotate, no infrastructure to provision, no vendor lock-in. Your configuration, your data, your control.

How to Connect RCSB PDB to Windsurf via MCP

Follow these steps to integrate the RCSB PDB MCP Server with Windsurf.

Open MCP Settings

Go to Settings → MCP Configuration or press Cmd+Shift+P and search "MCP"

Add the server

Paste the JSON configuration above into mcp_config.json

Save and reload

Windsurf will detect the new server automatically

Start using RCSB PDB

Open Cascade and ask: "Using RCSB PDB, help me...". 2 tools available

Why Use Windsurf with the RCSB PDB MCP Server

Windsurf provides unique advantages when paired with RCSB PDB through the Model Context Protocol.

Windsurf's Cascade agent autonomously chains multiple tool calls in sequence, solving complex multi-step tasks without manual intervention

Purpose-built for agentic workflows. Cascade understands context across your entire codebase and integrates MCP tools natively

JSON-based configuration means zero code changes: paste a URL, reload, and all 2 tools are immediately available

Real-time tool feedback is displayed inline, so you see API responses directly in your editor without switching contexts

RCSB PDB + Windsurf Use Cases

Practical scenarios where Windsurf combined with the RCSB PDB MCP Server delivers measurable value.

Automated code generation: ask Cascade to fetch data from RCSB PDB and generate models, types, or handlers based on real API responses

Live debugging: query RCSB PDB tools mid-session to inspect production data while debugging without leaving the editor

Documentation generation: pull schema information from RCSB PDB and have Cascade generate comprehensive API docs automatically

Rapid prototyping: combine RCSB PDB data with Cascade's code generation to scaffold entire features in minutes

RCSB PDB MCP Tools for Windsurf (2)

These 2 tools become available when you connect RCSB PDB to Windsurf via MCP:

get_pdb_structure

PDB IDs are 4-character codes like 1HHO, 6LU7, 7BNN. Get full structural details by PDB ID

search_pdb

Returns PDB ID, title, experimental method (X-ray, Cryo-EM, NMR), resolution, authors, and bound ligands. Essential for drug discovery and structural biology. Search 220K+ 3D molecular structures in the Protein Data Bank

Example Prompts for RCSB PDB in Windsurf

Ready-to-use prompts you can give your Windsurf agent to start working with RCSB PDB immediately.

"Show me the structure of the SARS-CoV-2 main protease."

"Get full structural details for PDB entry 1HHO — what protein is it?"

"Find all cryo-EM structures of ribosome complexes."

Troubleshooting RCSB PDB MCP Server with Windsurf

Common issues when connecting RCSB PDB to Windsurf through the Vinkius, and how to resolve them.

Server not connecting

Check Settings → MCP for the server status. Try toggling it off and on.

RCSB PDB + Windsurf FAQ

Common questions about integrating RCSB PDB MCP Server with Windsurf.

How does Windsurf discover MCP tools?

Windsurf reads the mcp_config.json file on startup and connects to each configured server via Streamable HTTP. Tools are listed in the MCP panel and available to Cascade automatically.

Can Cascade chain multiple MCP tool calls?

Yes. Cascade is an agentic system. it can plan and execute multi-step workflows, calling several tools in sequence to accomplish complex tasks without manual prompting between steps.

Does Windsurf support multiple MCP servers?

Yes. Add as many servers as needed in mcp_config.json. Each server's tools appear in the MCP panel and Cascade can use tools from different servers in a single flow.