How to Use the EBI PDBe MCP in Claude Code

Q: Is EBI PDBe setup complex in Claude Code?

It is straightforward. You run the claude mcp add command with the server URL, and it registers all tools for your terminal sessions.

Connect Claude Code to EBI PDBe for headless structural data extraction. Perfect for your CI/CD pipelines.

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Connect EBI PDBe MCP to Claude Code

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

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Headless Structural Querying

Claude Code utilizes `search_structures` to find PDB entries in your terminal. It outputs the results directly into your shell or log files. This is designed for automated workflows. You get structured data without needing a browser or GUI.

Programmatic Cofactor and Ligand Extraction

Pipe the output of `get_cofactors` or `get_ligand_monomers` into your analysis scripts. Claude Code retrieves these chemical components in seconds. This automates your docking preparation. You can process hundreds of structures by chaining these calls in a script.

Automated Publication and Citation Tracking

Use `get_publications` to automate the generation of reference lists. Claude Code fetches the primary citation for any PDB ID and saves it to your metadata files. This removes the manual work of tracking research sources. It keeps your documentation updated with every new structure processed.

Setup guide

Set up EBI PDBe MCP in Claude Code

Prerequisites

Claude Code CLI installed (npm install -g @anthropic-ai/claude-code)
Active Vinkius subscription with a valid endpoint token

1

Run the add command

Open your terminal and run the command shown on the right. Replace [YOUR_TOKEN_HERE] with your endpoint token from cloud.vinkius.com. Use --scope user to make it available across all projects.
2

Verify the connection

Start a Claude Code session and type /mcp to list connected servers. You should see ebi-pdbe-mcp with a green status indicator.
3

Start using tools

Ask Claude Code something like "Check my latest EBI PDBe transactions." It will automatically discover and invoke the available EBI PDBe tools.

Terminal

claude mcp add --transport http ebi-pdbe-mcp https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp

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Prerequisites

Claude Code CLI installed
Active Vinkius subscription with a valid endpoint token

1

Open the config file

Create or edit .mcp.json in your project root for project-level scope, or ~/.claude.json for user-level scope.
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

Restart Claude Code

Start a new Claude Code session. Type /mcp to confirm the server is connected. The tools will be automatically available in your conversation.

.mcp.json

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

Get your connection token →

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Common questions about EBI PDBe MCP in Claude Code

You can. Once the MCP Server is added, you use the CLI to request structural data. Claude Code runs the tools and prints the data to your console.

It calls the 16 available tools via the MCP transport. You can invoke them directly in your shell commands to fetch structural information.

It does. You can script the tool calls to run batch queries against the PDB, making it ideal for large-scale structural bioinformatics tasks.

It is straightforward. You run the `claude mcp add` command with the server URL, and it registers all tools for your terminal sessions.

The server acts as a local proxy for public data. It accesses the EBI API without exposing your environment, and it does not store your local data.

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

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