3D Cryo Electron Microscopy Community Challenges
Published December 21, 2017 | Version 1.1
Dataset Open

CryoEM Maps and Associated Data Submitted to the 2015/2016 EMDataBank Map Challenge

Creators

  • 1. Rutgers University, USA
  • 2. Stanford University, USA
  • 3. New York Structural Biology Center, USA
  • 4. Centro Nacional de Biotecnología, Madrid, ES
  • 5. Purdue University, USA
  • 6. EMBL European Bioinformatics Institute, UK
  • 7. University of Toronto, CA
  • 8. Francis Crick Institute, UK
  • 9. Chinese Academy of Sciences, CN
  • 10. Max Planck Institute for Biophysics, DE
  • 11. MRC Laboratory of Molecular Biology, UK
  • 12. Baylor College of Medicine, USA
  • 13. Oregon Health Sciences University, USA
  • 14. Institut de Biologia Molecular de Barcelona, ES
  • 15. HHMI Janelia Research Campus, USA
  • 16. École Polytechnique Fédérale de Lausanne, CH
  • 17. Institut de Biologie Structurale Grenoble, FR
  • 18. Utrecht University, NL
  • 19. National Institutes of Health, USA
  • 20. Wadsworth Laboratories, USA
  • 21. The Scripps Research Institute La Jolla, USA
  • 22. Netherlands Cancer Institute, NL
  • 23. Max Planck Institute for Biochemistry, Martinsreid, DE
  • 24. Texas A&M University, USA

Description

Files and metadata associated with the EMDataBank/Unified Data Resource for 3DEM 2015/2016 Map 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.

Seven benchmark raw image datasets were selected for the challenge. Six are selected from recently described single particle structure determinations with image data collected as multi-frame movies; one is based on simulated (in silico) images. All of the raw image datasets are archived at pdbe.org/empiar.

27 Challengers created 66 single particle reconstructions from the targets, and then uploaded their results with associated details.  15 of the reconstructions were calculated using the SDSC Gordon supercomputer.

This map 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 Map 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). A Directors Award from the UCSD Supercomputer Center provided supercomputer access that was used in 15 of the 66 submitted entries.

Files

1README.txt

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Additional details

Cites
10.1093/nar/gkv1126 (DOI)
10.1016/j.str.2011.12.014 (DOI)
10.1016/j.jsb.2016.02.008 (DOI)
Documents
http://challenges.emdataresource.org (URL)
References
10.6019/EMPIAR-10010 (DOI)
10.6019/EMPIAR-10012 (DOI)
10.6019/EMPIAR-10013 (DOI)
10.6019/EMPIAR-10026 (DOI)
10.6019/EMPIAR-10029 (DOI)
10.6019/EMPIAR-10025 (DOI)
10.6019/EMPIAR-10028 (DOI)
10.6019/EMPIAR-10005 (DOI)
10.6019/EMPIAR-10011 (DOI)

Funding

Unified Data Resource for 3DEM 5R01GM079429-07
National Institutes of Health

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
  • Marabini et al (2016) The Electron Microscopy Exchange (EMX) Iniitiative doi:10.1016/j.jsb.2016.02.008
  • Lawson and Chiu (2018) Comparing Cryo-EM Structures doi:10.1016/j.jsb.2018.10.004
  • Stagg and Mendez (2018) Processing apoferritin with the Appion pipeline doi:10.1016/j.jsb.2018.06.009
  • Heymann (2018) Single Particle reconstruction and validation using Bsoft for the map challenge doi:10.1016/j.jsb.2018.07.003
  • Sorzano et al (2018) A new algorithm for high-resolution reconstruction of single particles by electron microscopy doi:10.1016/j.jsb.2018.08.002
  • Bell et al (2018) New software tools in EMAN2 inspired by EMDatabank map challenge doi:10.1016/j.jsb.2018.09.002
  • Donati et al (2018) Fast multiscale reconstruction for Cryo-EM doi:10.1016/j.jsb.2018.09.008
  • Heymann (2018) Map Challenge assessment: Fair comparison of single particle cryoEM reconstructions doi:10.1016/j.jsb.2018.07.012
  • Jonic (2018) A methodology using Gaussian-based density map approximation to assess sets of cryo-electron microscopy density maps doi:10.1016/j.jsb.2018.07.014
  • Pintilie and Chiu (2018) Assessment of structural features in Cryo-EM density maps using SSE and side chain Z-scores doi:10.1016/j.jsb.2018.08.015
  • Marabini et al (2018) Map challenge: Analysis using a pair comparison method based on Fourier shell correlation doi:10.1016/j.jsb.2018.09.009
  • Mendez and Stagg (2018) Assessing the quality of single particle reconstructions by atomic model building doi:10.1016/j.jsb.2018.09.004
  • Heymann et al (2018) The first single particle analysis Map Challenge: A summary of the assessments doi:10.1016/j.jsb.2018.08.010

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