Dataset Open Access
CryoEM Maps and Associated Data Submitted to the 2015/2016 EMDataBank Map Challenge
Lawson, Catherine L.;
Chiu, Wah;
Carragher, Bridget;
Carazo, Jose-Maria;
Jiang, Wen;
Patwardhan, Ardan;
Rubinstein, John;
Rosenthal, Peter;
Sun, Fei;
Vonck, Janet;
Bai, Xiaochen;
Bell, James;
Caputo, Nick;
Chakraborty, Arka;
Chen, Dong-Hua;
Chen, James;
Diaz-Avalos, Ruben;
Donati, Laurene;
Estrozi, Leandro;
Galaz Montoya, Jesus;
Gati, Cornelius;
Gomez-Blanco, Josue;
Grigorieff, Nikolaus;
Gros, Piet;
Heymann, Bernard;
Leith, ArDean;
Li, Fei;
Ludtke, Steven;
Nans, Andrea;
Nilchian, Masih;
Punjabi, Ali;
Sixma, Titia;
Tegunov, Dimitry;
Yang, Kailu;
Yu, Guimei;
Zhang, Junjie;
Sala, Raul
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.
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1README.txt
md5:fa777a028ee7e5fa12fb6f076fbcb7df |
2.1 kB | Download |
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BetaGal_benchmark.zip
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6.0 GB | Download |
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BMV_benchmark.zip
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5.9 GB | Download |
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Ferritin_benchmark.zip
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706.1 MB | Download |
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GroEL_benchmark.zip
md5:6a426054a1c07e4b1a3d407ad09f3ea6 |
1.1 GB | Download |
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Images_for_all_benchmarks.zip
md5:41285fd0792235e5dd30c65c0ee34cfe |
707.2 MB | Download |
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Map Challenge Web Contents Archive.pdf
md5:f9099f2959fadfdb7be3587766d31ce2 |
1.5 MB | Download |
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map-challenge-metadata.xls
md5:c3addaa28698174757c5fa137d3e7cfe |
286.7 kB | Download |
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maps_revised2018.zip
md5:12faf1d1190909eaa58d725ad01d4b80 |
7.2 GB | Download |
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Proteasome_benchmark.zip
md5:de1d58f7854c6bdbbf2533f42700ec03 |
2.7 GB | Download |
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Ribosome_benchmark.zip
md5:1f51ea2a89defca85e64402a5bc4d04f |
8.4 GB | Download |
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TRPVI_benchmark.zip
md5:23ce888932ad212625b5df7c18bbf335 |
3.3 GB | Download |
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
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- Publication date:
- December 21, 2017
- DOI:
-
- Keyword(s):
- cryo electron microscopy cryoEM validation challenge benchmark
- Subject(s):
- Grants:
-
National Institutes of Health:
- Unified Data Resource for 3DEM (5R01GM079429-07)
- Related identifiers:
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- License (for files):
- Creative Commons Attribution 4.0 International