EMDB Web Resources

Curr Protoc Bioinformatics. 2018 Mar;61(1):5.10.1-5.10.12. doi: 10.1002/cpbi.48. Epub 2018 Apr 9.


The Electron Microscopy Data Bank (EMDB; http://emdb-empiar.org) is a global openly-accessible archive of biomolecular and cellular 3D reconstructions derived from electron microscopy (EM) data. EMBL-EBI develops web-based resources to facilitate the reuse of EMDB data. Here we provide protocols for how these resources can be used for searching EMDB, visualising EMDB structures, statistically analysing EMDB content and checking the validity of EMDB structures. Protocols for searching include quick link categories from the main page, links to latest entries released during the weekly cycle, filtered browsing of the entire archive and a form-based search. For visualisation, the 'Volume Slicer' enables slices of EMDB entries to be visualised interactively and in three orthogonal directions. The EMstats web service (https://emdb-empiar.org/emstats) provides up-to-date interactive statistical charts analysing EMDB. All EMDB entries have 'visual analysis' pages that provide basic validation information for the entry.

Keywords: Cryo-electron microscopy; EMDB; electron tomography; search; single particle image processing; structure; validation.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Databases as Topic*
  • Image Processing, Computer-Assisted
  • Internet*
  • Microscopy, Electron / methods*