MCP server

Pdbe

io.github.pipeworx-io/pdbe

Checked 26 Oct 2026, 08:29 UTC · Connected to it and listed its tools

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

Website Source

At a glance

Type

MCP server

Publisher

pipeworx.io (verified by the MCP Registry)

Status

Working at last check

Tools

45

Token cost

About 26,702 tokens per request

Sets up in

Claude Code, Claude Desktop, Codex, Gemini CLI, Cursor, VS Code, Antigravity, ChatGPT, OpenAI API, Grok

Last checked

26 Oct 2026, 08:29 UTC

Connect it to your agent

Add to CursorAdd to VS CodeVS Code Insiders

Opens the app, which shows the server and asks you to confirm. For other apps, copy the setup below.

Claude Code

claude mcp add --transport http pdbe https://gateway.pipeworx.io/pdbe/mcp

Claude Desktop

Settings → Connectors → Add custom connector, and paste the URL.

Codex (config.toml)

[mcp_servers.pdbe]
url = "https://gateway.pipeworx.io/pdbe/mcp"

Gemini CLI

{"mcpServers":{"pdbe":{"httpUrl":"https://gateway.pipeworx.io/pdbe/mcp"}}}

Cursor

{"mcpServers":{"pdbe":{"url":"https://gateway.pipeworx.io/pdbe/mcp"}}}

VS Code

{"servers":{"pdbe":{"type":"http","url":"https://gateway.pipeworx.io/pdbe/mcp"}}}

Antigravity

agy mcp add pdbe https://gateway.pipeworx.io/pdbe/mcp

ChatGPT

Settings → Apps & Connectors → Advanced settings: turn on Developer mode, then Create a connector and paste the URL. Which plans can do this varies.

OpenAI API (Responses tools)

{"type":"mcp","server_label":"pdbe","server_url":"https://gateway.pipeworx.io/pdbe/mcp","require_approval":"always"}

Grok (xAI API tools)

{"type":"mcp","server_label":"pdbe","server_url":"https://gateway.pipeworx.io/pdbe/mcp"}

Tools

• get_molecules ~126 tokens
  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".
• get_summary ~139 tokens
  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".
• uniprot_mappings ~134 tokens
  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".

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