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Pdbe

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

Code source Site web Documentation

Installation

Ajoutez ceci à la configuration MCP de votre client (Claude Desktop : claude_desktop_config.json ; Cursor : .cursor/mcp.json ; VS Code et les autres utilisent la même forme « mcpServers »).

Remote (streamable-http)
Claude Code 
claude mcp add --transport http pdbe 'https://gateway.pipeworx.io/pdbe/mcp'
Configuration JSON (Claude Desktop, Cursor, VS Code) 
{
    "mcpServers": {
        "pdbe": {
            "type": "http",
            "url": "https://gateway.pipeworx.io/pdbe/mcp"
        }
    }
}

Documentation

Tirée du README du projet sur GitHub, actualisée chaque semaine. Les liens ouvrent GitHub.

Sommaire
  1. mcp-pdbe
  2. Tools
  3. Quick Start
  4. No MCP client? Call it over HTTP
  5. Standalone (no gateway account)
  6. Using with ask_pipeworx
  7. More
  8. License

mcp-pdbe

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

Part of Pipeworx — an MCP gateway connecting AI agents to 1683+ live data sources.

Tools

ToolDescription
get_summaryPDBe (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_moleculesPDBe (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_mappingsPDBe (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 1683+ data sources. The only difference is which pack's tools are listed directly; ask_pipeworx reaches all of them from either one.

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":"..."}.

Standalone (no gateway account)

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-pdbe

It 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.

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

Questions fréquentes

Qu'est-ce que Pdbe ?

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

Comment installer Pdbe ?

Il fonctionne comme serveur distant. Dans Claude Code : claude mcp add --transport http pdbe 'https://gateway.pipeworx.io/pdbe/mcp'. Pour les autres clients, collez la configuration JSON de cette page dans leurs réglages MCP.

Faut-il une clé API pour Pdbe ?

Son entrée au registre n'indique aucune clé ni secret obligatoire. Certaines fonctions peuvent tout de même demander un compte auprès du service auquel il se connecte.

Pdbe est-il open source ?

Oui. Son code est sur GitHub sous licence MIT.

Qui maintient Pdbe ?

Il est publié par pipeworx-io. AI.tn le référence sans le maintenir ni le recommander.

Issu du registre MCP officiel. Être listé n'est pas une recommandation : vérifiez le code et les permissions d'un serveur avant de lui donner accès à vos données.