How to Use the EBI PDBe MCP in Cline

Q: How do I perform an EBI PDBe search in Cline?

You give Cline a natural language prompt. It executes searchstructures to find the correct PDB IDs and presents them to you for selection.

Q: Can I check quality with EBI PDBe in Cline?

You can. Ask Cline to run getqualityscores on any entry. It will provide the metrics so you can decide if the structure meets your research standards.

Cline fetches EBI PDBe structural data to build your bioinformatics tools. No manual lookups required.

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Connect EBI PDBe MCP to Cline

Create your Vinkius account to connect EBI PDBe to Cline 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 Cline

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Direct Structural Data Retrieval

Cline uses `get_summary` to verify PDB entries for your scripts. It checks resolution and experimental methods before proceeding with your task. This eliminates manual database navigation. Cline pulls the exact data you need for your structural analysis pipelines.

Automated Residue and Mutation Mapping

You can task Cline with `get_mutated_residues` or `get_modified_residues` to track non-standard amino acids. It writes the data into your project files automatically. This ensures your code accounts for engineered mutations. Cline handles the inventory of residues per chain without errors.

Sequence and Topology Discovery

Cline runs `get_secondary_structure` and `get_uniprot_mapping` to analyze protein folds. It maps these findings to your UniProt sequences instantly. This provides a clear link between structure and sequence. Cline uses these tools to build your data models with high precision.

Setup guide

Set up EBI PDBe MCP in Cline

Prerequisites

VS Code with Cline extension installed
Active Vinkius subscription with a valid endpoint token

1

Open Cline MCP settings

Click the Cline icon in the VS Code sidebar to open the Cline panel. Then click the MCP Servers icon (server stack) at the top-right corner of the panel.
2

Add a remote server

Click "Remote Servers" at the top, then click "Add Remote MCP". In the Name field, type ebi-pdbe-mcp. In the URL field, paste your Vinkius endpoint: https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp. Get your token from cloud.vinkius.com.
3

Enable the server

After saving, the server appears in the Cline MCP panel. Toggle the switch to enable it. The status indicator turns green when the connection is live.
4

Start using tools

Return to the Cline chat and ask: "Check my latest EBI PDBe refund status." Cline will discover the available tools and request your approval before invoking each one — giving you full control over every action.

Cline MCP Settings

{
  "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 Cline

You give Cline a natural language prompt. It executes `search_structures` to find the correct PDB IDs and presents them to you for selection.

Yes. Cline calls the relevant tools to fetch structural data and writes the corresponding analysis code into your repository.

You can. Ask Cline to run `get_quality_scores` on any entry. It will provide the metrics so you can decide if the structure meets your research standards.

Add the server URL in the MCP Settings tab. Once connected, Cline automatically discovers all 16 tools and starts using them.

The server only transmits structural query parameters to the public EBI database. No proprietary sequence data or analysis results are sent out.

Use it with your favorite AI tools

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

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