How to Use the EBI PDBe MCP in Cursor

Q: Can Cursor write code using EBI PDBe assembly data?

Yes, Cursor uses getassemblies to inspect quaternary structures. The agent reads the composition data and writes code that correctly handles multi-chain protein complexes.

Q: How does Cursor handle EBI PDBe cofactor annotations?

When you ask Cursor about enzyme catalysis, it runs getcofactors to find bound metal ions or prosthetic groups. It then uses this data to write accurate biochemical simulation parameters.

Generate biological code using live macromolecular data by connecting Cursor to the EBI PDBe MCP Server.

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Connect EBI PDBe MCP to Cursor

Create your Vinkius account to connect EBI PDBe to Cursor 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 Cursor

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Live Binding Site Data for Cursor Code Generation

When writing molecular docking scripts, let Cursor pull actual ligand coordinates instead of using placeholder data. Your agent runs `get_binding_sites` and `get_ligand_monomers` to inject real residue interactions and molecular weights directly into your active editor. This integration eliminates syntax errors when writing parsing logic for small molecules. Cursor reads the precise JSON output from the EBI PDBe endpoint, meaning your generated Python scripts match the actual API schema perfectly.

Map UniProt Coordinates in Cursor Agent Mode

Building bioinformatics pipelines in Cursor gets easier when your editor understands protein sequence mappings. The agent uses `get_uniprot_mapping` to resolve PDB chains to UniProt accessions, writing the integration code for you in real-time. If you need to verify structure topology, the editor calls `get_secondary_structure` to count helices and sheets. Cursor uses this structural breakdown to write precise visualization scripts or feature extraction routines.

Verify Structure Quality via this MCP Server

Do not let bad crystal structures ruin your machine learning training sets. While coding in Cursor, your agent can run `get_quality_scores` to check R-factor and resolution metrics for any PDB ID you reference in your code. If a structure fails your quality threshold, Cursor can automatically use `get_related_entries` to find alternative conformations or mutants. This lets you automate dataset curation directly within your development environment.

Setup guide

Set up EBI PDBe MCP in Cursor

Prerequisites

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

1

Open MCP Settings

Go to Cursor Settings → MCP or open the Command Palette (Cmd+Shift+P / Ctrl+Shift+P) and search for "MCP: Add Server".
2

Add the EBI PDBe MCP

Cursor will create or open .cursor/mcp.json in your project root. Paste the JSON snippet on the right. Replace [YOUR_TOKEN_HERE] with your endpoint token from cloud.vinkius.com.
3

Enable Agent mode

Open Composer (Cmd+I / Ctrl+I) and switch to Agent mode using the dropdown at the top. MCP tools are only available in Agent mode.
4

Verify the connection

Ask Cursor something like "List my recent EBI PDBe transactions." If the MCP tools are loaded correctly, Cursor will call the EBI PDBe tools automatically. You can also check Settings → MCP for a green status indicator.

.cursor/mcp.json

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

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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 Cursor

Add the server to your .cursor/mcp.json file under the mcpServers object. Once configured, Cursor Agent mode can call tools like search_structures to find and pull protein data directly into your workspace.

Yes, Cursor uses get_assemblies to inspect quaternary structures. The agent reads the composition data and writes code that correctly handles multi-chain protein complexes.

When you ask Cursor about enzyme catalysis, it runs get_cofactors to find bound metal ions or prosthetic groups. It then uses this data to write accurate biochemical simulation parameters.

Yes, you can ask the Cursor agent to find specific targets like insulin receptor. It executes search_structures on the EBI PDBe database and returns a list of matching PDB IDs directly to your chat.

No, only the specific PDB IDs or search terms you query are sent to the EBI servers. Cursor retrieves the macromolecular coordinates and metadata over secure HTTPS, keeping your local workspace and proprietary code files private.

Use it with your favorite AI tools

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

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