pdbe 3 tools

MCP server exposing 3 tools for pdbe.

Endpoint

This URL is a JSON-RPC 2.0 endpoint over HTTP. Issue POST requests with a JSON-RPC body. Browsers and search crawlers land here on GET.

POST https://gateway.pipeworx.io/pdbe/mcp
Content-Type: application/json

{"jsonrpc":"2.0","id":1,"method":"tools/list"}

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".

Code samples (curl / TypeScript / one-click client install), schemas, and the live playground are on the pack page:
https://pipeworx.io/packs/pdbe/

Pipeworx is an open MCP gateway connecting AI agents to live data. pipeworx.io