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EMDataBank specifications


Unique identifier OMICS_08960
Name EMDataBank
Restrictions to use None
Maintained Yes


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Publications for EMDataBank

EMDataBank citations


Validation of Structures in the Protein Data Bank

PMCID: 5718880
PMID: 29174494
DOI: 10.1016/j.str.2017.10.009
call_split See protocol

[…] The PDF reports are organized as follows. The title page displays the wwPDB logo (and also the EMDataBank logo for EM entries), specifies the type of the report (whether it is preliminary, confidential, or produced for a publicly available PDB entry), shows basic administrative information abou […]


Electrostatic interaction between polyglutamylated tubulin and the nexin–dynein regulatory complex regulates flagellar motility

Mol Biol Cell
PMCID: 5555654
PMID: 28637765
DOI: 10.1091/mbc.E17-05-0285
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[…] off value of 0.5 were ∼5.0 nm (Supplemental Figure S2B). Surface renderings were generated using UCSF Chimera (). The electron microscopic maps of averaged DMTs are available at the EM Data Bank (www.emdatabank.org) under the accession numbers EMD-6753–6756. […]


Modeling Beta Traces for Beta Barrels from Cryo EM Density Maps

Biomed Res Int
PMCID: 5259677
PMID: 28164115
DOI: 10.1155/2017/1793213

[…] d to generate β-barrel density maps at 10 Å resolution using the pdb2mrc function in EMAN [], with a sampling of 1 Å/pixel. The experimental cryo-EM density maps were downloaded from EMDB (http://www.emdatabank.org/). Since atomic structures are available for such cryo-EM maps, the density region that corresponds to one chain of the protein was first segmented using the atomic structure as an enve […]


Model based local density sharpening of cryo EM maps

PMCID: 5679758
PMID: 29058676
DOI: 10.7554/eLife.27131.036

[…] Unfiltered reconstructions for TRPV1 (EMD-5778), γ-secretase (EMD-3061) and β-galactosidase (EMD-2984) were obtained from the EMDB model challenge website (http://challenges.emdatabank.org). Initial map targets for coordinate refinement were generated by applying uniform filtering to the original EMDB entries. The deposited map for TRPV1 (EMD-5778) was globally sharpened […]


Using the Volta phase plate with defocus for cryo EM single particle analysis

PMCID: 5279940
PMID: 28109158
DOI: 10.7554/eLife.23006.013
call_split See protocol

[…] The reconstructed 3D density maps from the Relion particle polishing and MotionCor2 data processing workflows were deposited to the EMDataBank with accession codes EMD-3455 and EMD-3456 respectively. The dataset was deposited to the Electron Microscopy Pilot Image Archive with accession code EMPIAR-10078. […]


Empowering pharmacoinformatics by linked life science data

J Comput Aided Mol Des
PMCID: 5385323
PMID: 27830428
DOI: 10.1007/s10822-016-9990-4

[…] Protein Data Bank in Europe (PDBe), Protein Data Bank Japan (PDBj), the Biological Magnetic Resonance Data Bank (http://www.bmrb.wisc.edu/; BMRB []), and the Electron Microscopy Data Bank (http://www.emdatabank.org; EMDataBank []). In addition to those, small-molecule organic and metal–organic crystal structures are deposited in the Cambridge Structural Database (http://www.ccdc.cam.ac.uk/; CSD [, […]


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EMDataBank institution(s)
Department of Chemistry and Chemical Biology and Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, NJ; Department of Biochemistry and Molecular Biology, National Center for Macromolecular Imaging, Verna and Marrs McLean, Baylor College of Medicine, Houston, TX, USA; Protein Data Bank in Europe, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK; Department of Computer Science, Rice University, Houston, TX, USA
EMDataBank funding source(s)
EMDataBank Unified Data Resource for 3DEM is supported by the National Institutes of Health [R01GM079429] to Baylor College of Medicine, Rutgers University and the EMBL-European Bioinformatics Institute. PDBe receives additional support for EMDB development from the UK Medical Research Council [MR/L007835]; European Commission Framework 7 Programme [284209]; Wellcome Trust [088944, 104948]; EMBL-EBI.

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