Summary
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.
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mcp-pdbe
PDBe (Protein Data Bank in Europe, EBI) MCP.
Part of Pipeworx — an MCP gateway connecting AI agents to 1476+ live data sources.
Tools
| Tool | Description |
|---|---|
get_summary | PDBe (Protein Data Bank in Europe, EBI): get a PDB entry summary — title, experimental method, release date, source organism, and entity counts (polypeptide/ligand/water/...). Keyless. The EBI counterpart to RCSB PDB. Pass a 4-char PDB id like "1cbs". |
get_molecules | PDBe (EBI): list the molecules/entities in a PDB structure — proteins, nucleic acids, and ligands, each with entity_id, molecule_type, name, and chain length. Keyless. Pass a 4-char PDB id like "1cbs". |
uniprot_mappings | PDBe (EBI): SIFTS cross-database mapping of a PDB structure to UniProt — for each UniProt accession, the matching chains and residue range. Curated cross-database mappings unique to EBI. Keyless. Pass a 4-char PDB id like "1cbs". |
Quick Start
Add to your MCP client (Claude Desktop, Cursor, Windsurf, etc.):
{
"mcpServers": {
"pdbe": {
"url": "https://gateway.pipeworx.io/pdbe/mcp"
}
}
}
What this endpoint actually serves
tools/list at https://gateway.pipeworx.io/pdbe/mcp returns the tools in the table
above plus the shared Pipeworx meta-tools — ask_pipeworx,
discover_tools, search_within, remember/recall and the rest of the
gateway-wide set. So the tool count you see is larger than this table: a
single-pack endpoint currently lists roughly 30 shared tools alongside the
pack's own. The connection's initialize response states its exact scope, and
is the authoritative answer for a given day.
This is deliberate, not multiplexing by accident. The meta-tools are what let a
scoped connection answer a question this pack does not cover — via
ask_pipeworx, which routes across the whole catalog — without you adding a
second MCP server. There is currently no way to mount a pack endpoint without
them; if the extra schemas cost you more context than the routing is worth,
connect to the full gateway once rather than to several pack endpoints.
Or connect to the full Pipeworx gateway to get every pack's tools listed directly, instead of just this one's:
{
"mcpServers": {
"pipeworx": {
"url": "https://gateway.pipeworx.io/mcp"
}
}
}
Both URLs reach the same gateway and the same 1476+ data sources. The
only difference is which pack's tools are listed directly; ask_pipeworx
reaches all of them from either one.
Using with ask_pipeworx
Instead of calling tools directly, you can ask questions in plain English — this works on the pack endpoint above as well as on the full gateway:
ask_pipeworx({ question: "your question about Pdbe data" })
The gateway picks the right tool and fills the arguments automatically.
More
License
MIT
No MCP client? Call it over HTTP
curl -X POST https://gateway.pipeworx.io/v1/tools/pdbe_get_summary \
-H 'Content-Type: application/json' \
-d '{"pdb_id":"1cbs"}'
No account needed for the first calls. Inspect any tool: GET https://gateway.pipeworx.io/v1/tools/pdbe_get_summary. Find one: POST https://gateway.pipeworx.io/v1/tools/search_packs with {"query":"..."}.
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