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emdb-database

Search and retrieve cryo-EM density maps and metadata from EMDB via REST API.

298|27|Updated Feb 18, 2026
Search Tags:#bioinformatics#drug discovery#density map#structural biology#cryo-em#emdb
One-click install
npx skills add https://github.com/jaechang-hits/SciAgent-Skills --skill emdb-database
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: emdb-database
Source: https://github.com/jaechang-hits/SciAgent-Skills/tree/main/skills/structural-biology-drug-discovery/emdb-database
Command: npx skills add https://github.com/jaechang-hits/SciAgent-Skills --skill emdb-database

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires requests, pandas, matplotlib, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill provides programmatic access to the Electron Microscopy Data Bank (EMDB), enabling users to search for and retrieve cryo-EM density maps, fitted atomic models, and associated metadata.

Core Features & Use Cases

  • Search EMDB: Find cryo-EM density maps by keywords, resolution, method, or organism.
  • Retrieve Map Info: Get download URLs for .map.gz density files and associated PDB models.
  • Fetch Metadata: Obtain detailed entry information, including resolution, reconstruction method, and publications.
  • Use Case: You need to find all available cryo-EM density maps for the SARS-CoV-2 spike protein with a resolution better than 3.0 Å. This Skill can query EMDB, filter the results, and provide a list of relevant entries with their download links.

Quick Start

Use the emdb-database skill to search for cryo-EM maps of the 'ribosome 70S bacterial' and print the first 5 results.

Frequently Asked Questions about emdb-database

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I search the EMDB for cryo-EM density maps by resolution and organism?▼

You can search cryo-EM density maps in the EMDB by querying keywords, resolution, reconstruction method, or organism. The Skill fetches matching entries and their associated metadata directly via the EMDB REST API.

Can I retrieve PDB cross-references and download URLs for fitted atomic models from EMDB?▼

Yes, you can retrieve PDB cross-references and download URLs for fitted atomic models from the EMDB. The Skill fetches entry details including publication information and direct links to .map.gz density files.

What is the best way to find SARS-CoV-2 spike protein cryo-EM maps with a resolution better than 3.0 Å?▼

The best way to find SARS-CoV-2 spike protein cryo-EM maps with a resolution better than 3.0 Å is querying the EMDB by keyword and resolution. This filters relevant entries and provides their download links.

Do I need pandas and matplotlib to access cryo-EM density map metadata?▼

Yes, you need pandas and matplotlib to access and process cryo-EM density map metadata. The Skill requires these dependencies along with requests for data handling, querying, and visualizing structural biology results.

What specific metadata fields are returned when fetching cryo-EM entry details from the EMDB?▼

When fetching cryo-EM entry details from the EMDB, the metadata returned includes resolution, reconstruction method, and publication information. It also provides map download URLs and PDB cross-references for structural biology analysis.

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