PDBe

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PDBe (Protein Data Bank in Europe, EBI) MCP.

3 tools
0ms auth
free tier 50 calls/day

Tools

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 counter

No parameters required.

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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"

No parameters required.

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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

No parameters required.

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Test with curl

The gateway speaks JSON-RPC 2.0 over HTTP POST. You can test any pack directly from the terminal.

List available tools
bash 
curl -X POST https://gateway.pipeworx.io/pdbe/mcp \
  -H "Content-Type: application/json" \
  -d '{"jsonrpc":"2.0","id":1,"method":"tools/list"}'
Call a tool
bash 
curl -X POST https://gateway.pipeworx.io/pdbe/mcp \
  -H "Content-Type: application/json" \
  -d '{"jsonrpc":"2.0","id":2,"method":"tools/call","params":{"name":"get_summary","arguments":{}}}'

Use with the SDK

Install @pipeworx/sdk to call tools from any TypeScript/Node project.

TypeScript 
import { Pipeworx } from '@pipeworx/sdk';
const px = new Pipeworx();
const result = await px.call("get_summary", {});
ask_pipeworx 
// Or ask in plain English:
const answer = await px.ask("pdbe (protein data bank in europe, ebi) mcp");