Connects Claude to PDBe, the European node of the Protein Data Bank hosted by EBI. Part of the Pipeworx gateway ecosystem, which offers an ask_pipeworx tool that lets you query protein structure data in plain English rather than constructing API calls manually. The source doesn't list specific tools, but this is aimed at researchers and developers working with protein structure data who want to pull PDB entries, search molecular structures, or retrieve crystallography metadata without leaving their AI chat interface. Available as a standalone server or through the full Pipeworx gateway that bundles 836+ data sources.
PDBe (Protein Data Bank in Europe, EBI) MCP.
Part of Pipeworx — an MCP gateway connecting AI agents to 836+ live data sources.
| Tool | Description |
|---|
Add to your MCP client (Claude Desktop, Cursor, Windsurf, etc.):
{
"mcpServers": {
"pdbe": {
"url": "https://gateway.pipeworx.io/pdbe/mcp"
}
}
}
Or connect to the full Pipeworx gateway for access to all 836+ data sources:
{
"mcpServers": {
"pipeworx": {
"url": "https://gateway.pipeworx.io/mcp"
}
}
}
Instead of calling tools directly, you can ask questions in plain English:
ask_pipeworx({ question: "your question about Pdbe data" })
The gateway picks the right tool and fills the arguments automatically.
MIT
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