How to Use the EBI PDBe MCP in Windsurf

Q: Does it show the sequence mapping for EBI PDBe in Windsurf?

Absolutely. Use getuniprotmapping to align PDB chains with UniProt accessions. It bridges the gap between sequence databases and structural files.

Get structural biology data directly in Windsurf. Cascade reads PDB entries and maps them to your code without context switching.

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Connect EBI PDBe MCP to Windsurf

Create your Vinkius account to connect EBI PDBe to Windsurf and route execution through our secure gateway. The platform manages server hosting, runtime updates, and security layers. Configuration requires no manual server provisioning.

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Setup EBI PDBe with Windsurf

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Perplexity

Automated Protein Structure Lookup

Cascade triggers `get_summary` to pull metadata for any PDB ID. It identifies the experimental method and resolution before you write a single line of code. This MCP Server provides the exact entry details. You get titles, authors, and experimental context immediately within the IDE.

Functional Site Analysis

Use `get_binding_sites` and `get_ligand_monomers` to map small molecule interactions. Cascade parses these outputs to suggest docking parameters or validation logic. It connects biological findings to your local files. You see how ligands interact with specific residues without leaving your workspace.

Quaternary Assembly Identification

Cascade executes `get_assemblies` to determine if your protein acts as a monomer or a complex. It helps you clarify the stoichiometry of your biological models. This tool reveals the physical state of the structure. You can verify if the assembly matches your expected functional unit.

Setup guide

Set up EBI PDBe MCP in Windsurf

Prerequisites

Windsurf IDE installed (macOS, Windows, or Linux)
Active Vinkius subscription with a valid endpoint token

1

Open MCP configuration

Click the Cascade assistant icon in the sidebar, then click the hammer icon (🔨) at the top of the panel. Select "Configure" to open ~/.codeium/windsurf/mcp_config.json.
2

Add the EBI PDBe MCP

Paste the JSON snippet shown on the right into the mcpServers object. Replace [YOUR_TOKEN_HERE] with your endpoint token from cloud.vinkius.com.
3

Refresh MCPs

Go back to the hammer icon (🔨) in Cascade and click "Refresh". Windsurf will detect the new server. No full restart is needed — the connection is hot-reloaded.
4

Verify in Cascade

Start a new Cascade conversation and ask something like "Show my EBI PDBe payment history." If connected, Cascade will call the EBI PDBe tools directly. You will see a green dot next to the server name in the MCP panel.

mcp_config.json

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

Get your connection token →

Independent Platform Disclaimer: Vinkius is an independent platform and is not affiliated with, endorsed by, sponsored by, verified by, or otherwise authorized by PDBe (Protein Data Bank in Europe). All third-party trademarks, logos, and brand names are the property of their respective owners. Their use on this website is strictly for informational purposes to identify service compatibility and interoperability.

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Common questions about EBI PDBe MCP in Windsurf

Yes. You just ask Cascade to search for a protein by name or function. It uses `search_structures` to return relevant IDs directly into your chat.

The server exposes 16 tools that Cascade calls as needed. You don't manage the connection; the IDE handles the data flow once you add the endpoint.

It pulls directly from the official PDB source. You can check `get_quality_scores` to verify resolution and R-factor for any entry you pull.

Absolutely. Use `get_uniprot_mapping` to align PDB chains with UniProt accessions. It bridges the gap between sequence databases and structural files.

Your files never leave your machine. This MCP Server only sends requested PDB IDs to the public EBI API, keeping your codebase and research data local.

Use it with your favorite AI tools

Connect this server to Cursor, Claude, VS Code, and more.

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