Emdb

MCP server · by pipeworx-io

Developer Tools npmStreamable HTTP v0.2.2

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

View source ↗ Website ↗ Generate config for multiple servers More servers

Install

Pin version registry version 0.2.2

npm
npx -y @pipeworx/mcp-emdb

npm
npx -y @pipeworx/mcp-emdb@0.2.2

Streamable HTTP
https://gateway.pipeworx.io/emdb/mcp

Setup by client

Pick your client — the config below is generated for this server (both local and hosted-endpoint forms). Copy respects the “Pin version” switch above.

claude_desktop_config.json

{
  "mcpServers": {
    "emdb": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-emdb"
      ],
      "env": {
        "PIPEWORX_API_KEY": "<YOUR_PIPEWORX_API_KEY>"
      }
    }
  }
}

{
  "mcpServers": {
    "emdb": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-emdb@0.2.2"
      ],
      "env": {
        "PIPEWORX_API_KEY": "<YOUR_PIPEWORX_API_KEY>"
      }
    }
  }
}

Remote (hosted) endpoint

https://gateway.pipeworx.io/emdb/mcp

Claude Desktop: Settings → Connectors → Add custom connector, paste this URL.

Format verified against the official Claude Desktop docs ↗.

terminal

claude mcp add --env PIPEWORX_API_KEY=<YOUR_PIPEWORX_API_KEY> emdb -- npx -y @pipeworx/mcp-emdb

claude mcp add --env PIPEWORX_API_KEY=<YOUR_PIPEWORX_API_KEY> emdb -- npx -y @pipeworx/mcp-emdb@0.2.2

terminal

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

Format verified against the official Claude Code docs ↗.

.cursor/mcp.json

{
  "mcpServers": {
    "emdb": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-emdb"
      ],
      "env": {
        "PIPEWORX_API_KEY": "<YOUR_PIPEWORX_API_KEY>"
      }
    }
  }
}

{
  "mcpServers": {
    "emdb": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-emdb@0.2.2"
      ],
      "env": {
        "PIPEWORX_API_KEY": "<YOUR_PIPEWORX_API_KEY>"
      }
    }
  }
}

.cursor/mcp.json (hosted endpoint)

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

Format verified against the official Cursor docs ↗.

.vscode/mcp.json

{
  "servers": {
    "emdb": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-emdb"
      ],
      "env": {
        "PIPEWORX_API_KEY": "<YOUR_PIPEWORX_API_KEY>"
      }
    }
  }
}

{
  "servers": {
    "emdb": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-emdb@0.2.2"
      ],
      "env": {
        "PIPEWORX_API_KEY": "<YOUR_PIPEWORX_API_KEY>"
      }
    }
  }
}

.vscode/mcp.json (hosted endpoint)

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

Format verified against the official VS Code docs ↗.

mcp_config.json

{
  "mcpServers": {
    "emdb": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-emdb"
      ],
      "env": {
        "PIPEWORX_API_KEY": "<YOUR_PIPEWORX_API_KEY>"
      }
    }
  }
}

{
  "mcpServers": {
    "emdb": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-emdb@0.2.2"
      ],
      "env": {
        "PIPEWORX_API_KEY": "<YOUR_PIPEWORX_API_KEY>"
      }
    }
  }
}

mcp_config.json (hosted endpoint)

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

Format verified against the official Windsurf docs ↗.

Environment variables

Defined in the server's official registry manifest. Required secrets are shown as <YOUR_…> placeholders in the configs above.

PIPEWORX_API_KEY secret — Optional Pipeworx API key. Without it calls are anonymous and capped daily; a free key raises the cap.

GitHub

⭐ 1 stars · 最近更新于 47 天前 · MIT license

About this server

mcp emdb EMDB (EBI Electron Microscopy Data Bank) MCP — keyless. Part of Pipeworx — an MCP gateway connecting AI agents to 1683+ live data sources. Tools Tool Description search maps Search the EBI Electron Microscopy Data Bank (EMDB) for 3D cryo EM / electron tomography density maps by free text ke…

Summary from the project README — github.com/pipeworx-io/mcp-emdb

Distributed as npm, Streamable HTTP, listed under Developer Tools. Review our MCP security guide before granting access to real data.

Frequently asked questions

What does the Emdb MCP server do?

How do I install Emdb?

Run the install command shown above, then paste the config for your client (Claude Desktop, Claude Code, Cursor, VS Code or Windsurf) into its MCP settings and restart the client.

Is Emdb free to use?

The MCP server itself is free to install. The source is public on https://github.com/pipeworx-io/mcp-emdb. Any third-party service it calls may require its own API key and account.

Which clients support Emdb?

Any MCP-compatible client can use it, including Claude Desktop, Claude Code, Cursor, VS Code, Windsurf and custom agents.

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