MCP server

Emdb

io.github.pipeworx-io/emdb

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

EMDB (EBI Electron Microscopy Data Bank) MCP — keyless.

Website Source

At a glance

Type

MCP server

Publisher

pipeworx.io (verified by the MCP Registry)

Status

Working at last check

Tools

44

Token cost

About 26,641 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 emdb https://gateway.pipeworx.io/emdb/mcp

Claude Desktop

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

Codex (config.toml)

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

Gemini CLI

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

Cursor

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

VS Code

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

Antigravity

agy mcp add emdb https://gateway.pipeworx.io/emdb/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":"emdb","server_url":"https://gateway.pipeworx.io/emdb/mcp","require_approval":"always"}

Grok (xAI API tools)

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

Tools

• get_map ~134 tokens
  Get a single EMDB entry by its EMDB id (e.g. "EMD-1080"). Returns a trimmed record: title, sample, structure-determination method, resolution (Angstrom), and release date. EMDB holds 3D electron-microscopy density maps of proteins, complexes, and viruses. Keyless.
• search_maps ~204 tokens
  Search the EBI Electron Microscopy Data Bank (EMDB) for 3D cryo-EM / electron-tomography density maps by free-text keyword (e.g. "ribosome", "spike protein", "apoptosis"). Returns matching maps with EMDB id, title, resolution (Angstrom), and structure-determination method. Keyless. Complements PDB/A

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