drug-discovery-prompts/upstream/K-Dense-AI-scientific-agent-skills/skills/database-lookup/references/emdb.md

title, task, lineage_type, upstream_source, upstream_sha, imported_at, prompt_class, upstream_changes, author, validated

title	task	lineage_type	upstream_source	upstream_sha	imported_at	prompt_class	upstream_changes	author	validated
EMDB (Electron Microscopy Data Bank)		import	https://github.com/K-Dense-AI/scientific-agent-skills/blob/9c9bd2e9/skills/database-lookup/references/emdb.md	9c9bd2e9	2026-06-26	prompt	accepted	upstream	false

EMDB (Electron Microscopy Data Bank)

Base URL

https://www.ebi.ac.uk/emdb/api/

Auth

No auth required.

Key Endpoints

Endpoint	Description
/entry/{emdb_id}	Full entry metadata (e.g. EMD-1234)
/entry/map/{emdb_id}	Map/volume metadata
/entry/experiment/{emdb_id}	Experimental details
/entry/fitted/{emdb_id}	Fitted PDB models
/search/{query}?rows={n}	Search entries by keyword

Example Calls

# Entry metadata
https://www.ebi.ac.uk/emdb/api/entry/EMD-1234

# Search for ribosome entries
https://www.ebi.ac.uk/emdb/api/search/ribosome?rows=5

# Experimental details
https://www.ebi.ac.uk/emdb/api/entry/experiment/EMD-1234

Response Format

JSON. Search includes pagination and matching entry array.

Rate Limits

EBI fair-use policy. Map files (MRC/CCP4) available via FTP for bulk access.