3D Cryo Electron Microscopy Community Challenges

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Published January 24, 2018 | Version 1
Dataset Open

CryoEM Models and Associated Data Submitted to the 2015/2016 EMDataBank Model Challenge

Creators

  • 1. Rutgers University, USA
  • 2. UC Davis, USA
  • 3. Stanford University, USA
  • 4. Lawrence Berkeley Laboratory, USA
  • 5. EMBL-European Bioinformatics Institute, UK
  • 6. University of Cambridge, UK
  • 7. University of Basel, CH
  • 8. Birkbeck College, UK
  • 9. UC Los Angeles, USA
  • 10. Baylor College of Medicine, USA
  • 11. Forschungszentrum Jülich, DE
  • 12. University of Tokyo, JP
  • 13. National Insititutes of Health, USA
  • 14. Queensland University of Technology, AU
  • 15. University of Washington, USA
  • 16. Inria/CNRS, FR
  • 17. Birbeck College, UK
  • 18. Purdue University, USA
  • 19. National Institutes of Health, USA
  • 20. University of Illinois Urbana-Champaign, USA
  • 21. tUniversity of Illinois Urbana-Champaign, USAemp
  • 22. Los Alamos National Laboratory, USA

Description

Files and metadata associated with the EMDataBank/Unified Data Resource for 3DEM 2015/2016 Models Challenge hosted at challenges.emdatabank.org are deposited.

All members of the Scientific Community--at all levels of experience--were invited to participate as Challengers, and/or as Assessors.

Eight recently determined target structures were selected for the challenge. All of the maps were archived in the EM Data Bank (EMDB; http://emdatabank.org).

In total 16 Challengers created 106 models and uploaded their results with associated details.  In the zip files, each entry is represented in a folder containing the original deposition upload (deposited_EM.pdb), initial processing at RCSB/Rutgers (deposited_EM_edited.pdb, maxit.cif, maxit.cif.pdb) and final model version evaluated (model-compare.pdb) at UC Davis (http://model-compare.emdatabank.org).

This model challenge was one of two community-wide challenges sponsored by EMDataBank in 2015/2016 to critically evaluate 3DEM methods that are coming into use, with the ultimate goal of developing validation criteria associated with every 3DEM map and map-derived model.

 

Notes

The 2015/2016 Model Challenge was supported by the US National Institutes of Health / National Institute for General Medical Sciences (NIH/NIGMS) Under Grant Number R01 GM079429 to Wah Chiu (PI).

Files

BetaGalactosidase_mapA.zip

Files (3.9 GB)

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Additional details

Related works

Cites
10.1093/nar/gkv1126 (DOI)
10.1016/j.jsb.2016.02.008 (DOI)
http://model-compare.emdatabank.org (URL)
Documents
http://challenges.emdatabank.org (URL)

References

  • Henderson et al (2012) Outcome of the first electron microscopy validation task force meeting. doi:10.1016/j.str.2011.12.014
  • Lawson et al (2016) EMDataBank unified data resource for 3DEM. doi:10.1093/nar/gkv1126

Subjects

Benchmarking
https://meshb.nlm.nih.gov/record/ui?name=Benchmarking
Databases, Protein
https://meshb.nlm.nih.gov/record/ui?name=Databases,%20Protein
Cryoelectron Microscopy
https://meshb.nlm.nih.gov/record/ui?name=Cryoelectron%20Microscopy
Imaging, Three Dimensional
https://meshb.nlm.nih.gov/record/ui?name=Imaging,%20Three%20Dimensional
Microscopy, Electron
https://meshb.nlm.nih.gov/record/ui?name=Microscopy,%20Electron
Models, Molecular
https://meshb.nlm.nih.gov/record/ui?ui=D008958