CryoEM Maps and Associated Data Submitted to the 2015/2016 EMDataBank Map Challenge
Creators
- Lawson, Catherine1
- Chiu, Wah2
- Carragher, Bridget3
- Carazo, Jose-Maria4
- Jiang, Wen5
- Patwardhan, Ardan6
- Rubinstein, John7
- Rosenthal, Peter8
- Sun, Fei9
- Vonck, Janet10
- Bai, Xiaochen11
- Bell, James12
- Caputo, Nick13
- Chakraborty, Arka14
- Chen, Dong-Hua2
- Chen, James13
- Diaz-Avalos, Ruben15
- Donati, Laurene16
- Estrozi, Leandro17
- Galaz Montoya, Jesus12
- Gati, Cornelius11
- Gomez-Blanco, Josue4
- Grigorieff, Nikolaus15
- Gros, Piet18
- Heymann, Bernard19
- Leith, ArDean20
- Li, Fei21
- Ludtke, Steven12
- Nans, Andrea8
- Nilchian, Masih16
- Punjabi, Ali7
- Sixma, Titia22
- Tegunov, Dimitry23
- Yang, Kailu24
- Yu, Guimei5
- Zhang, Junjie24
- Sala, Raul1
- 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
Files
BetaGal_benchmark.zip
Files
(28.9 GB)
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Additional details
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
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