Dataset Open Access
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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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> <creator> <creatorName>Jiang, Wen</creatorName> <affiliation>Purdue University, USA</affiliation> </creator> <creator> <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> </creator> <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> </creator> <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> </creator> <creator> <creatorName>Leith, ArDean</creatorName> <affiliation>Wadsworth Laboratories, USA</affiliation> </creator> <creator> <creatorName>Li, Fei</creatorName> <affiliation>The Scripps Research Institute La Jolla, USA</affiliation> </creator> <creator> <creatorName>Ludtke, Steven</creatorName> <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-1903-1574</nameIdentifier> <affiliation>Baylor College of Medicine, USA</affiliation> </creator> <creator> <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&M University, USA</affiliation> </creator> <creator> <creatorName>Yu, Guimei</creatorName> <affiliation>Purdue University, USA</affiliation> </creator> <creator> <creatorName>Zhang, Junjie</creatorName> <affiliation>Texas A&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"><p>Files and metadata associated with the EMDataBank/Unified Data Resource for 3DEM 2015/2016 Map Challenge hosted at challenges.emdatabank.org are deposited.</p> <p>All members of the Scientific Community--at all levels of experience--were invited to participate as Challengers, and/or as Assessors.</p> <p>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.</p> <p>27 Challengers created 66 single particle reconstructions from the targets, and then uploaded their results with associated details.&nbsp; 15 of the reconstructions were calculated using the SDSC Gordon supercomputer.</p> <p>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.</p> <p>&nbsp;</p></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> </descriptions> </resource>
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