# Emdb [Health: Active]

**Category:** 🧬 Biology & Bioinformatics  
**Repository:** https://github.com/pipeworx-io/mcp-emdb  
**GitHub Stars:** 1  
**npm Downloads (last month):** 411  
**Views:** 1  
**Installs:** 0  
**Upvotes:** 0  
**Directory Page:** https://allmcps.com/mcp/emdb

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

## Tools
Capabilities this server exposes over MCP:

- **search_maps** — 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/AlphaFold (which hold atomic/experimental structures).
- **get_map** — 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.

## Claude Desktop Quick Installation
Install path detected from listing signals. Uses `npx` (confidence: high):

```json
"mcpServers": {
  "emdb": {
    "command": "npx",
    "args": ["-y","@pipeworx/mcp-emdb"],
    "env": {
      "PIPEWORX_API_KEY": "",
      "PIPEWORX_META_TOOLS": "",
      "NODE_USE_ENV_PROXY": ""
    }
  }
}
```

**Requires environment variables:** `PIPEWORX_API_KEY`, `PIPEWORX_META_TOOLS`, `NODE_USE_ENV_PROXY` — the values above are empty placeholders; fill in real credentials before running (see the repository for what each one is for).

## Documentation

## 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:

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

The local npm option uses `npx`:

```json
{
  "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.

_Full upstream README: https://allmcps.com/mcp/emdb/readme_