How to Use the EBI PDBe MCP in Claude

Q: How does Claude Desktop handle large residue listings from EBI PDBe?

The getresiduelisting tool returns a sample of the first 20 residues per chain to prevent token bloat. This keeps your Claude Desktop context window clean while still providing enough sequence structure for the model to understand the layout.

Q: Can Claude Desktop identify modified residues in EBI PDBe entries?

Yes, the agent calls getmodifiedresidues to locate non-standard nucleotides or amino acids. It matches parent compounds and modification names, displaying them directly in your chat.

Pull 3D macromolecular structures and ligand data directly into your Claude Desktop chat using the EBI PDBe MCP Server.

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Connect EBI PDBe MCP to Claude Desktop

Create your Vinkius account to connect EBI PDBe to Claude Desktop 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 Claude Desktop

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Search and Summarize PDB Structures

Stop leaving your Claude Desktop app to look up protein files on the web. Let your agent run `search_structures` to find relevant entries using simple English queries, then grab the core details with `get_summary`. You get resolution, authors, and experimental methods right inside your chat window without context switching. If you need to verify the experimental setup, Claude Desktop calls `get_experiment` to check the exact physical parameters. This means you can spot low-resolution data or inappropriate experimental methods before you base your entire modeling workflow on a bad file.

Mapping Sequences in Claude Desktop

Your agent can map physical structure coordinates to biological sequences without manual translation. By running `get_uniprot_mapping` inside Claude Desktop, the model instantly connects PDB chains to UniProt accession numbers and exact residue ranges. To verify sequence alterations in the crystallized construct, the model uses `get_mutated_residues` to flag engineered mutations. You see exactly where the lab modified the wild-type sequence, allowing Claude Desktop to write highly accurate sequence annotations.

Analyze Assemblies and Binding Sites with this MCP Server

To understand functional states, Claude Desktop calls `get_assemblies` to check if a protein operates as a monomer or a complex. You get a clear breakdown of entity counts and preferred quaternary states directly in your workspace. When evaluating drug targets, the model invokes `get_binding_sites` and `get_ligand_monomers` to map out exact residue interactions with small molecules. This lets Claude Desktop pinpoint pocket locations and molecular weights without you parsing raw MMCIF files.

Setup guide

Set up EBI PDBe MCP in Claude Web or Desktop

1

Open Claude Settings

Go to claude.ai, click your profile icon, then navigate to Customize → Connectors.
2

Add Custom Connector

Click the "+" button and select Add custom connector. Paste your Vinkius endpoint URL: https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp Replace [YOUR_TOKEN_HERE] with your token from cloud.vinkius.com. For OAuth-protected servers, expand Advanced settings to add credentials.
3

Start a conversation

Open a new chat. The EBI PDBe MCP tools are available immediately — no restart needed.

Endpoint URL

https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp

No configuration file needed — paste the URL directly in the Claude web interface.

Available on Free (1 connector), Pro, Max, Team, and Enterprise plans.

Prerequisites

Claude Desktop installed (macOS or Windows)
Active Vinkius subscription with a valid endpoint token

1

Open Claude Desktop Settings

Click the menu icon at the top-left corner, go to Settings → Developer → Edit Config. This opens claude_desktop_config.json in your default text editor.
2

Paste the EBI PDBe MCP configuration

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

Restart Claude Desktop

Close and reopen the application. Claude needs a full restart to load new MCPs — refreshing a conversation is not enough.
4

Verify the connection

Open a new conversation. Click the 🔌 icon at the bottom of the message input. You should see tools listed under ebi-pdbe-mcp.

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 Claude Desktop

Open your Claude Desktop configuration file and add the server configuration under the mcpServers key. Once you restart the app, the agent will have immediate access to tools like get_summary and search_structures during your research sessions.

Yes, you can ask the agent to verify structural reliability. It will run get_quality_scores to fetch global validation metrics, helping you filter out poor structures right inside Claude Desktop.

The get_residue_listing tool returns a sample of the first 20 residues per chain to prevent token bloat. This keeps your Claude Desktop context window clean while still providing enough sequence structure for the model to understand the layout.

Yes, the agent calls get_modified_residues to locate non-standard nucleotides or amino acids. It matches parent compounds and modification names, displaying them directly in your chat.

No, your queries only go to the official European Bioinformatics Institute endpoints. Claude Desktop processes the returned PDB structural metadata locally or within your secure session, ensuring your target sequence coordinates remain confidential.

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