Mcp Emdb — independently scanned and version-tracked by SaferSkills.
SaferSkills independently audited Mcp Emdb (Agent Skill) and scored it 100/100 (green). The audit ran 55 deterministic rules across Security, Supply Chain, Maintenance, Transparency, and Community; it found 0 high-severity and 0 lower-severity findings. The full rule-by-rule trace and per-finding evidence are below. Free, methodology-open.
Findings & checks · 0 flagged
Every scanned point with the score it earned and what moved between them.
First recorded scan — no prior version to compare against.
The primary manifest — the file an agent reads to learn what this artifact does.
EMDB (EBI Electron Microscopy Data Bank) MCP — keyless.
Part of Pipeworx — an MCP gateway connecting AI agents to 1878+ live data sources. This is an independent, unofficial integration — not affiliated with, endorsed by, or published by the upstream provider.
| Tool | Description |
|---|---|
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. |
Add to your MCP client (Claude Desktop, Cursor, Windsurf, etc.):
{
"mcpServers": {
"emdb": {
"url": "https://gateway.pipeworx.io/emdb/mcp"
}
}
}tools/list at https://gateway.pipeworx.io/emdb/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 1878+ data sources. The only difference is which pack's tools are listed directly; ask_pipeworx reaches all of them from either one.
curl -X POST https://gateway.pipeworx.io/v1/tools/search_maps \
-H 'Content-Type: application/json' \
-d '{"query":"ribosome"}'No account needed for the first calls. Inspect any tool: GET https://gateway.pipeworx.io/v1/tools/search_maps. Find one: POST https://gateway.pipeworx.io/v1/tools/search_packs with {"query":"..."}.
This package also runs as a local stdio MCP server — no Pipeworx account, no gateway round-trip:
{
"mcpServers": {
"emdb": {
"command": "npx",
"args": ["-y", "@pipeworx/mcp-emdb"]
}
}
}Or run it directly to confirm it starts:
npx -y @pipeworx/mcp-emdbIt 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.
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 Emdb data" })The gateway picks the right tool and fills the arguments automatically.
MIT
~30 seconds. Free. No account. Every finding cites a rule and a line of evidence.