EMDB Web Resources

Current Protocols in Bioinformatics
Sanja AbbottArdan Patwardhan

Abstract

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.

References

Nov 6, 2002·Trends in Biochemical Sciences·Mohamed TagariKim Henrick
Oct 12, 2013·Journal of Structural Biology·Ingvar LagerstedtGerard J Kleywegt
Nov 30, 2013·Nucleic Acids Research·Aleksandras GutmanasGerard J Kleywegt
Feb 16, 2016·Journal of Structural Biology·José Salavert-TorresArdan Patwardhan
Aug 31, 2016·Methods in Enzymology·A Patwardhan, C L Lawson
Jun 6, 2017·Acta Crystallographica. Section D, Structural Biology·Ardan Patwardhan

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Citations

Oct 26, 2018·Nucleic Acids Research·UNKNOWN wwPDB consortium
Jun 28, 2019·GigaScience·Lu GanShujun Cai
Nov 7, 2019·Nucleic Acids Research·David R ArmstrongSameer Velankar
Feb 1, 2020·Structural Dynamics·Catherine L LawsonWah Chiu
Sep 4, 2020·Protein Science : a Publication of the Protein Society·Eric F PettersenThomas E Ferrin
Dec 22, 2020·Briefings in Bioinformatics·Vaishali P WamanChristine Orengo
Oct 8, 2019·Structure·Ross HartmanC Martin Lawrence
May 8, 2021·The Journal of Biological Chemistry·Mitchell D Miller, George N Phillips
Nov 3, 2021·Acta Crystallographica. Section D, Structural Biology·Adam J SimpkinRonan M Keegan
Dec 7, 2021·Acta Crystallographica. Section D, Structural Biology·Brinda VallatHelen M Berman

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