EMPIAR: a public archive for raw electron microscopy image data

By Andrii Iudin, Paul K. Korir, J. Salavert-Torres, Gerard J. Kleywegt, Ardan Patwardhan. Nature Methods, 2016

299 citations recorded by the source corpus.

Subfields: Radiation, Structural Biology, Surfaces, Coatings and Films

View Paper: https://www.semanticscholar.org/paper/a7663ab3d08781ee21f7170f6740179c268a5838

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Radiation

1. Sjors H. W. Scheres
2. Dari Kimanius
3. Erik Lindahl
4. W. Hagen
5. Takanori Nakane
6. Jasenko Zivanov
7. Björn Forsberg

In Structural Biology

1. Dari Kimanius
2. Erik Lindahl
3. Takanori Nakane
4. Sjors H. W. Scheres
5. Björn Forsberg
6. W. Hagen
7. Jasenko Zivanov
8. David J. Fleet

In Surfaces, Coatings and Films

1. Dari Kimanius
2. Erik Lindahl
3. Takanori Nakane
4. Björn Forsberg
5. Jasenko Zivanov
6. W. Hagen
7. Sjors H. W. Scheres
8. David J. Fleet

Citations in the corpus

• Search and sequence analysis tools services from EMBL-EBI in 2022 (2022, unknown): “Since the last update, Open Targets (15), VarSite (16), PDBe-KB (17), GWAS Catalog (18), EMPIAR (19), European Variation Archive Studies (20) and Cellosaurus (21) have been added as new resources.”
• Helical reconstruction in RELION (2016, unknown): “Three of these data sets are available from the EMPIAR data base (Iudin et al., 2016): EMPIAR-10020 on tobacco mosaic virus (TMV) (Fromm et al., 2015); EMPIAR-10019 of the contractile sheath of the bacterial type-VI secretion system, which is composed of the proteins VipA/VipB (Kudryashev et al.,…”
• Protein Data Bank: the single global archive for 3D macromolecular structure data (2018, methodology): “The OneDep system also allows Data Depositors to provide additional links to other experimental data, housed in repositories such as SBGRID (sbgrid.org) (10), IIRMC (proteindiffraction.org) (11), SASBDB (www.sasbdb.org) (12) and EMPIAR (www. ebi.ac.uk/pdbe/emdb/empiar) (13).”
• Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive (2017, methodology): “Voluntary archival deposition of raw 3DEM images is currently supported by EMPIAR [34].”
• New tools for automated high-resolution cryo-EM structure determination in RELION-3 (2018, methodology): “DOI: https://doi.org/10.7554/eLife.42166.009 particle images of the P22 virion capsid protein ( Hryc et al., 2017 ), which we downloaded from EMPIAR-10083 ( Iudin et al., 2016 ).”
• PDBe: improved findability of macromolecular structure data in the PDB (2019, methodology): “PDBe previously introduced the Raw Experimental Data web component (19) to provide a summary and links to the raw experimental data from the Electron Microscopy Public Image Archive (EMPIAR) (44), SBGrid Data Bank (45) and Integrated Resource for Reproducibility in Macromolecular Crystallography (IR”
• Characterisation of molecular motions in cryo-EM single-particle data by multi-body refinement in RELION (2018, methodology): “This data set is available as entry 10028 on the EMPIAR data base (Iudin et al., 2016) and is used as a standard benchmark for RELION.”
• Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2 (2016, methodology): “empiar (Iudin et al., 2016) entry 10028 was used to assess performance, using refinements of 105k ribosomal particles in 3602-pixel images.”