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

Lawson, Catherine; 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

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      <creatorName>Lawson, Catherine</creatorName>
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      <affiliation>Rutgers University, USA</affiliation>
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      <creatorName>Chiu, Wah</creatorName>
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      <affiliation>Stanford University, USA</affiliation>
    </creator>
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      <creatorName>Carragher, Bridget</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-0624-5020</nameIdentifier>
      <affiliation>New York Structural Biology Center, USA</affiliation>
    </creator>
    <creator>
      <creatorName>Carazo, Jose-Maria</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0003-0788-8447</nameIdentifier>
      <affiliation>Centro Nacional de Biotecnología, Madrid, ES</affiliation>
    </creator>
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      <creatorName>Jiang, Wen</creatorName>
      <affiliation>Purdue University, USA</affiliation>
    </creator>
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      <creatorName>Patwardhan, Ardan</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0001-7663-9028</nameIdentifier>
      <affiliation>EMBL European Bioinformatics Institute, UK</affiliation>
    </creator>
    <creator>
      <creatorName>Rubinstein, John</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0003-0566-2209</nameIdentifier>
      <affiliation>University of Toronto, CA</affiliation>
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    <creator>
      <creatorName>Rosenthal, Peter</creatorName>
      <affiliation>Francis Crick Institute, UK</affiliation>
    </creator>
    <creator>
      <creatorName>Sun, Fei</creatorName>
      <affiliation>Chinese Academy of Sciences, CN</affiliation>
    </creator>
    <creator>
      <creatorName>Vonck, Janet</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0001-5659-8863</nameIdentifier>
      <affiliation>Max Planck Institute for Biophysics, DE</affiliation>
    </creator>
    <creator>
      <creatorName>Bai, Xiaochen</creatorName>
      <affiliation>MRC Laboratory of Molecular Biology, UK</affiliation>
    </creator>
    <creator>
      <creatorName>Bell, James</creatorName>
      <affiliation>Baylor College of Medicine, USA</affiliation>
    </creator>
    <creator>
      <creatorName>Caputo, Nick</creatorName>
      <affiliation>Oregon Health Sciences University, USA</affiliation>
    </creator>
    <creator>
      <creatorName>Chakraborty, Arka</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-9699-3208</nameIdentifier>
      <affiliation>Institut de Biologia Molecular de Barcelona, ES</affiliation>
    </creator>
    <creator>
      <creatorName>Chen, Dong-Hua</creatorName>
      <affiliation>Stanford University, USA</affiliation>
    </creator>
    <creator>
      <creatorName>Chen, James</creatorName>
      <affiliation>Oregon Health Sciences University, USA</affiliation>
    </creator>
    <creator>
      <creatorName>Diaz-Avalos, Ruben</creatorName>
      <affiliation>HHMI Janelia Research Campus, USA</affiliation>
    </creator>
    <creator>
      <creatorName>Donati, Laurene</creatorName>
      <affiliation>École Polytechnique Fédérale de Lausanne, CH</affiliation>
    </creator>
    <creator>
      <creatorName>Estrozi, Leandro</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0003-2548-2547</nameIdentifier>
      <affiliation>Institut de Biologie Structurale Grenoble, FR</affiliation>
    </creator>
    <creator>
      <creatorName>Galaz Montoya, Jesus</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-0113-9325</nameIdentifier>
      <affiliation>Baylor College of Medicine, USA</affiliation>
    </creator>
    <creator>
      <creatorName>Gati, Cornelius</creatorName>
      <affiliation>MRC Laboratory of Molecular Biology, UK</affiliation>
    </creator>
    <creator>
      <creatorName>Gomez-Blanco, Josue</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-6168-3859</nameIdentifier>
      <affiliation>Centro Nacional de Biotecnología, Madrid, ES</affiliation>
    </creator>
    <creator>
      <creatorName>Grigorieff, Nikolaus</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-1506-909X</nameIdentifier>
      <affiliation>HHMI Janelia Research Campus, USA</affiliation>
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    <creator>
      <creatorName>Gros, Piet</creatorName>
      <affiliation>Utrecht University, NL</affiliation>
    </creator>
    <creator>
      <creatorName>Heymann, Bernard</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-8872-5326</nameIdentifier>
      <affiliation>National Institutes of Health, USA</affiliation>
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    <creator>
      <creatorName>Leith, ArDean</creatorName>
      <affiliation>Wadsworth Laboratories, USA</affiliation>
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    <creator>
      <creatorName>Li, Fei</creatorName>
      <affiliation>The Scripps Research Institute La Jolla, USA</affiliation>
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      <creatorName>Ludtke, Steven</creatorName>
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      <affiliation>Baylor College of Medicine, USA</affiliation>
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      <creatorName>Nans, Andrea</creatorName>
      <affiliation>Francis Crick Institute, UK</affiliation>
    </creator>
    <creator>
      <creatorName>Nilchian, Masih</creatorName>
      <affiliation>École Polytechnique Fédérale de Lausanne, CH</affiliation>
    </creator>
    <creator>
      <creatorName>Punjabi, Ali</creatorName>
      <affiliation>University of Toronto, CA</affiliation>
    </creator>
    <creator>
      <creatorName>Sixma, Titia</creatorName>
      <affiliation>Netherlands Cancer Institute, NL</affiliation>
    </creator>
    <creator>
      <creatorName>Tegunov, Dimitry</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0001-7019-3221</nameIdentifier>
      <affiliation>Max Planck Institute for Biochemistry, Martinsreid, DE</affiliation>
    </creator>
    <creator>
      <creatorName>Yang, Kailu</creatorName>
      <affiliation>Texas A&amp;M University, USA</affiliation>
    </creator>
    <creator>
      <creatorName>Yu, Guimei</creatorName>
      <affiliation>Purdue University, USA</affiliation>
    </creator>
    <creator>
      <creatorName>Zhang, Junjie</creatorName>
      <affiliation>Texas A&amp;M University, USA</affiliation>
    </creator>
    <creator>
      <creatorName>Sala, Raul</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-6500-6441</nameIdentifier>
      <affiliation>Rutgers University, USA</affiliation>
    </creator>
  </creators>
  <titles>
    <title>CryoEM Maps and Associated Data Submitted to the 2015/2016 EMDataBank Map Challenge</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2017</publicationYear>
  <subjects>
    <subject>cryo electron microscopy</subject>
    <subject>cryoEM</subject>
    <subject>validation</subject>
    <subject>challenge</subject>
    <subject>benchmark</subject>
    <subject subjectScheme="url">https://meshb.nlm.nih.gov/record/ui?name=Benchmarking</subject>
    <subject subjectScheme="url">https://meshb.nlm.nih.gov/record/ui?name=Databases,%20Protein</subject>
    <subject subjectScheme="url">https://meshb.nlm.nih.gov/record/ui?name=Cryoelectron%20Microscopy</subject>
    <subject subjectScheme="url">https://meshb.nlm.nih.gov/record/ui?name=Imaging,%20Three%20Dimensional</subject>
    <subject subjectScheme="url">https://meshb.nlm.nih.gov/record/ui?name=Microscopy,%20Electron</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2017-12-21</date>
  </dates>
  <language>en</language>
  <resourceType resourceTypeGeneral="Dataset"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/1120379</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="Cites">10.1093/nar/gkv1126</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="Cites">10.1016/j.str.2011.12.014</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="References">10.6019/EMPIAR-10010</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="References">10.6019/EMPIAR-10012</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="References">10.6019/EMPIAR-10013</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="References">10.6019/EMPIAR-10026</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="References">10.6019/EMPIAR-10029</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="References">10.6019/EMPIAR-10025</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="References">10.6019/EMPIAR-10028</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="References">10.6019/EMPIAR-10005</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="References">10.6019/EMPIAR-10011</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="URL" relationType="Documents">http://challenges.emdatabank.org</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="Cites">10.1016/j.jsb.2016.02.008</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsPartOf">10.5281/zenodo.1120378</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsPartOf">https://zenodo.org/communities/3dcryoemchallenges</relatedIdentifier>
  </relatedIdentifiers>
  <version>1</version>
  <rightsList>
    <rights rightsURI="http://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;Files and metadata associated with the EMDataBank/Unified Data Resource for 3DEM 2015/2016 Map Challenge hosted at challenges.emdatabank.org are deposited.&lt;/p&gt;

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

&lt;p&gt;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.&lt;/p&gt;

&lt;p&gt;27 Challengers created 66 single particle reconstructions from the targets, and then uploaded their results with associated details.&amp;nbsp; 15 of the reconstructions were calculated using the SDSC Gordon supercomputer.&lt;/p&gt;

&lt;p&gt;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.&lt;/p&gt;

&lt;p&gt;&amp;nbsp;&lt;/p&gt;</description>
    <description descriptionType="Other">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.</description>
    <description descriptionType="Other">{"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"]}</description>
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Publication date:
December 21, 2017
DOI:
10.5281/zenodo.1120379

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Keyword(s):
cryo electron microscopy cryoEM validation challenge benchmark
Subject(s):
Benchmarking
Databases, Protein
Cryoelectron Microscopy
Imaging, Three Dimensional
Microscopy, Electron
Related identifiers:
Cites:
10.1093/nar/gkv1126, 10.1016/j.str.2011.12.014, 10.1016/j.jsb.2016.02.008
Documents:
http://challenges.emdatabank.org
References:
10.6019/EMPIAR-10010, 10.6019/EMPIAR-10012, 10.6019/EMPIAR-10013, 10.6019/EMPIAR-10026, 10.6019/EMPIAR-10029, 10.6019/EMPIAR-10025, 10.6019/EMPIAR-10028, 10.6019/EMPIAR-10005, 10.6019/EMPIAR-10011
Communities:
License (for files):
Creative Commons Attribution 4.0 International

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