Emdb

What Emdb does

Emdb exposes selected EMDB metadata through MCP. EMDB contains three-dimensional electron-microscopy density maps covering proteins, molecular complexes, and viruses. The integration is useful for locating map records and checking core metadata without downloading or processing density-map files.

Two domain tools are available:

• search_maps accepts a free-text query such as ribosome, spike protein, or apoptosis. Results include the EMDB identifier, title, resolution in Angstroms, and structure-determination method.
• get_map accepts an EMDB identifier such as EMD-1080. It returns a reduced record containing the title, sample, structure-determination method, resolution, and release date.

The service is an unofficial integration and is not affiliated with, endorsed by, or published by the upstream provider.

How it works

The hosted MCP endpoint is https://gateway.pipeworx.io/emdb/mcp. An MCP client connects to that URL and can invoke the Emdb tools over the gateway. The same gateway also provides shared Pipeworx meta-tools, including ask_pipeworx, discover_tools, search_within, and memory-related tools. A scoped Emdb connection therefore lists more tools than the two domain-specific tools; the exact set is returned during MCP initialization.

The gateway can also be used at https://gateway.pipeworx.io/mcp for direct access to all catalog packs. Alternatively, the HTTP interface supports calls such as POST /v1/tools/search_maps with a JSON body containing a query value.

For local MCP deployments, @pipeworx/mcp-emdb runs as a stdio bridge. The bridge forwards requests to the hosted Emdb endpoint, so it requires network access and has no offline mode.

Setup and configuration

Add the hosted endpoint to an MCP client with the emdb server name:

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

The local npm option uses npx:

{
  "mcpServers": {
    "emdb": {
      "command": "npx",
      "args": ["-y", "@pipeworx/mcp-emdb"]
    }
  }
}

Anonymous use requires no key and is limited to 50 calls per day. Setting PIPEWORX_API_KEY enables an account-based allowance of 200 calls per day through a free account. Set PIPEWORX_META_TOOLS=1 for the local bridge if the shared gateway tools should also be listed. When using an HTTPS proxy, newer Node.js releases can use it with NODE_USE_ENV_PROXY=1.

Tools and capabilities

• Search EMDB records using natural free-text keywords.
• Retrieve selected metadata for an individual EMDB accession.
• Connect through hosted streamable MCP, local stdio, or HTTP tool requests.
• Use ask_pipeworx to route plain-language questions across the wider Pipeworx catalog when the shared meta-tools are enabled or available through the gateway.
• Work without an EMDB-specific API key.

Limitations and notes

Results are metadata-oriented: the documented tools return record details rather than density-map files or full structural analysis. The local package depends on the hosted gateway and cannot operate offline. Anonymous gateway use is rate-limited to 50 calls per day; an account and API key raise the stated allowance to 200 calls per day. The endpoint also exposes shared Pipeworx tools, so the tool list can be larger than the Emdb-specific tool set.