Click on "Deploy Server".
Wait a few minutes for the server to deploy. Once ready, it will show a "Started" state.
In the chat, type @ followed by the MCP server name and your instructions, e.g., "@PDBe MCP Server get the summary for PDB entry 1cbs"
That's it! The server will respond to your query, and you can continue using it as needed.
Here is a step-by-step guide with screenshots.
PDBe (Protein Data Bank in Europe, EBI) MCP.
Part of Pipeworx — an MCP gateway connecting AI agents to 1683+ live data sources.
Tool | Description |
| 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". |
| 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". |
| 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". |
Related MCP server: Structural Biology MCP Server
Add to your MCP client (Claude Desktop, Cursor, Windsurf, etc.):
{
"mcpServers": {
"pdbe": {
"url": "https://gateway.pipeworx.io/pdbe/mcp"
}
}
}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 1683+ data sources. The
only difference is which pack's tools are listed directly; ask_pipeworx
reaches all of them from either one.
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":"..."}.
This package also runs as a local stdio MCP server — no Pipeworx account, no gateway round-trip:
{
"mcpServers": {
"pdbe": {
"command": "npx",
"args": ["-y", "@pipeworx/mcp-pdbe"]
}
}
}Or run it directly to confirm it starts:
npx -y @pipeworx/mcp-pdbeIt speaks MCP over stdin/stdout and answers initialize/tools/list/tools/call
for only this pack's tools — none of the shared meta-tools the gateway
connection above adds. Same source, same tools, no ask_pipeworx routing.
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.
MIT
This server cannot be deployed
Connect AI clients to biomedical data and tools.
Protein analysis: ESM-2/ESMC embeddings, mutation scoring, landscape scans, ESMFold structure.
Protein research over UniProtKB — search by function, fetch curated records, map IDs, proteomes.
Machine-readable entity discovery with provenance, trust and verified source evidence.
