Dataset Open Access

2019 EMDataResource Model Metrics Challenge Dataset

Lawson, Catherine L; Kryshtafovych, Andriy; Adams, Paul D; Afonine, Pavel V; Baker, Matthew L; Barad, Benjamin A; Bond, Paul; Burnley, Tom; Cao, Renzhi; Cheng, Jianlin; Chojnowski, Grzegorz; Cowtan, Kevin; Dill, Ken; DiMaio, Frank; Farrell, Daniel P; Fraser, James S; Herzik, Mark A Jr; Hoh, Soon Wen; Hou, Jie; Hung, Li-Wei; Igaev, Maxim; Joseph, Agnel P; Kihara, Daisuke; Kumar, Dilip; Mittal, Sumit; Monastryrskyy, Bohdan; Olek, Mateusz; Palmer, Colin M; Patwardhan, Ardan; Perez, Alberto; Pfab, Jonas; Pintilie, Greg D; Richardson, Jane S; Sarkar, Daipayan; Schäfer, Luisa U; Schmid, Michael F; Schröder, Gunnar F; Shekhar, Mrinal; Si, Dong; Singharoy, Abishek; Terashi, Genki; Terwilliger, Thomas C; Vaiana, Andrea; Wang, Liguo; Wankowicz, Stephanie A; Williams, Christopher J; Winn, Martyn; Wu, Tianqi; Yu, Xiaodi; Zhang, Kaiming; Berman, Helen M; Chiu, Wah


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      <creatorName>Adams, Paul D</creatorName>
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      <creatorName>Afonine, Pavel V</creatorName>
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      <creatorName>Baker, Matthew L</creatorName>
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      <creatorName>Barad, Benjamin A</creatorName>
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      <creatorName>Bond, Paul</creatorName>
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      <creatorName>Burnley, Tom</creatorName>
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      <creatorName>Cao, Renzhi</creatorName>
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      <affiliation>Pacific Lutheran University</affiliation>
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      <creatorName>Cheng, Jianlin</creatorName>
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      <creatorName>Cowtan, Kevin</creatorName>
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      <affiliation>University of York</affiliation>
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    <creator>
      <creatorName>Dill, Ken</creatorName>
      <givenName>Ken</givenName>
      <familyName>Dill</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-2390-2002</nameIdentifier>
      <affiliation>Stony Brook University</affiliation>
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    <creator>
      <creatorName>DiMaio, Frank</creatorName>
      <givenName>Frank</givenName>
      <familyName>DiMaio</familyName>
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      <affiliation>University of Washington Seattle</affiliation>
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      <creatorName>Farrell, Daniel P</creatorName>
      <givenName>Daniel P</givenName>
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      <creatorName>Fraser, James S</creatorName>
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      <affiliation>University of California San Francisco</affiliation>
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      <creatorName>Herzik, Mark A Jr</creatorName>
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      <creatorName>Hoh, Soon Wen</creatorName>
      <givenName>Soon Wen</givenName>
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      <affiliation>University of York</affiliation>
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      <creatorName>Hou, Jie</creatorName>
      <givenName>Jie</givenName>
      <familyName>Hou</familyName>
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      <affiliation>Saint Louis University</affiliation>
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    <creator>
      <creatorName>Hung, Li-Wei</creatorName>
      <givenName>Li-Wei</givenName>
      <familyName>Hung</familyName>
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      <affiliation>Los Alamos National Laboratory</affiliation>
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      <creatorName>Igaev, Maxim</creatorName>
      <givenName>Maxim</givenName>
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      <affiliation>Max Planck Institute for Biophysical Chemistry</affiliation>
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      <creatorName>Joseph, Agnel P</creatorName>
      <givenName>Agnel P</givenName>
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      <creatorName>Kihara, Daisuke</creatorName>
      <givenName>Daisuke</givenName>
      <familyName>Kihara</familyName>
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      <affiliation>Purdue University</affiliation>
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      <creatorName>Kumar, Dilip</creatorName>
      <givenName>Dilip</givenName>
      <familyName>Kumar</familyName>
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      <affiliation>Baylor College of Medicine</affiliation>
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      <creatorName>Mittal, Sumit</creatorName>
      <givenName>Sumit</givenName>
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      <creatorName>Olek, Mateusz</creatorName>
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      <creatorName>Palmer, Colin M</creatorName>
      <givenName>Colin M</givenName>
      <familyName>Palmer</familyName>
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      <affiliation>UKRI Science and Technology Facilities Council</affiliation>
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      <creatorName>Patwardhan, Ardan</creatorName>
      <givenName>Ardan</givenName>
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      <affiliation>European Bioinformatics Institute</affiliation>
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      <creatorName>Perez, Alberto</creatorName>
      <givenName>Alberto</givenName>
      <familyName>Perez</familyName>
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      <affiliation>University of Florida</affiliation>
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      <creatorName>Pfab, Jonas</creatorName>
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      <creatorName>Pintilie, Greg D</creatorName>
      <givenName>Greg D</givenName>
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      <creatorName>Richardson, Jane S</creatorName>
      <givenName>Jane S</givenName>
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      <affiliation>Duke University</affiliation>
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      <creatorName>Sarkar, Daipayan</creatorName>
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      <familyName>Sarkar</familyName>
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      <affiliation>Purdue University</affiliation>
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    <creator>
      <creatorName>Schäfer, Luisa U</creatorName>
      <givenName>Luisa U</givenName>
      <familyName>Schäfer</familyName>
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      <creatorName>Schmid, Michael F</creatorName>
      <givenName>Michael F</givenName>
      <familyName>Schmid</familyName>
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      <affiliation>Stanford University</affiliation>
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      <creatorName>Schröder, Gunnar F</creatorName>
      <givenName>Gunnar F</givenName>
      <familyName>Schröder</familyName>
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      <affiliation>Heinrich Heine University Düsseldorf</affiliation>
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    <creator>
      <creatorName>Shekhar, Mrinal</creatorName>
      <givenName>Mrinal</givenName>
      <familyName>Shekhar</familyName>
      <affiliation>Broad Institute of MIT and Harvard</affiliation>
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    <creator>
      <creatorName>Si, Dong</creatorName>
      <givenName>Dong</givenName>
      <familyName>Si</familyName>
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      <affiliation>University of Washington Bothell</affiliation>
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      <creatorName>Singharoy, Abishek</creatorName>
      <givenName>Abishek</givenName>
      <familyName>Singharoy</familyName>
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      <affiliation>Arizona State University</affiliation>
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      <creatorName>Terashi, Genki</creatorName>
      <givenName>Genki</givenName>
      <familyName>Terashi</familyName>
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      <affiliation>Purdue University</affiliation>
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    <creator>
      <creatorName>Terwilliger, Thomas C</creatorName>
      <givenName>Thomas C</givenName>
      <familyName>Terwilliger</familyName>
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      <affiliation>New Mexico Consortium</affiliation>
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      <creatorName>Vaiana, Andrea</creatorName>
      <givenName>Andrea</givenName>
      <familyName>Vaiana</familyName>
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      <affiliation>Max Planck Institute for Biophysical Chemistry</affiliation>
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    <creator>
      <creatorName>Wang, Liguo</creatorName>
      <givenName>Liguo</givenName>
      <familyName>Wang</familyName>
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      <affiliation>University of Washington Seattle</affiliation>
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      <creatorName>Wankowicz, Stephanie A</creatorName>
      <givenName>Stephanie A</givenName>
      <familyName>Wankowicz</familyName>
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      <affiliation>University of California San Francisco</affiliation>
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      <creatorName>Williams, Christopher J</creatorName>
      <givenName>Christopher J</givenName>
      <familyName>Williams</familyName>
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      <affiliation>Duke University</affiliation>
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    <creator>
      <creatorName>Winn, Martyn</creatorName>
      <givenName>Martyn</givenName>
      <familyName>Winn</familyName>
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      <affiliation>UKRI Science and Technology Facilities Council</affiliation>
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    <creator>
      <creatorName>Wu, Tianqi</creatorName>
      <givenName>Tianqi</givenName>
      <familyName>Wu</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-1545-3462</nameIdentifier>
      <affiliation>University of Missouri</affiliation>
    </creator>
    <creator>
      <creatorName>Yu, Xiaodi</creatorName>
      <givenName>Xiaodi</givenName>
      <familyName>Yu</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0001-7520-0646</nameIdentifier>
      <affiliation>Janssen Research and Development</affiliation>
    </creator>
    <creator>
      <creatorName>Zhang, Kaiming</creatorName>
      <givenName>Kaiming</givenName>
      <familyName>Zhang</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0003-0414-4776</nameIdentifier>
      <affiliation>Stanford University</affiliation>
    </creator>
    <creator>
      <creatorName>Berman, Helen M</creatorName>
      <givenName>Helen M</givenName>
      <familyName>Berman</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-3337-0660</nameIdentifier>
      <affiliation>Rutgers University</affiliation>
    </creator>
    <creator>
      <creatorName>Chiu, Wah</creatorName>
      <givenName>Wah</givenName>
      <familyName>Chiu</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-8910-3078</nameIdentifier>
      <affiliation>Stanford University</affiliation>
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  </creators>
  <titles>
    <title>2019 EMDataResource Model Metrics Challenge Dataset</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2020</publicationYear>
  <subjects>
    <subject>cryo-EM</subject>
    <subject>model validation</subject>
    <subject>3D structure</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2020-10-28</date>
  </dates>
  <language>en</language>
  <resourceType resourceTypeGeneral="Dataset"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/4148789</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.4148788</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsPartOf">https://zenodo.org/communities/3dcryoemchallenges</relatedIdentifier>
  </relatedIdentifiers>
  <rightsList>
    <rights rightsURI="https://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;This is the full dataset of the 2019 Cryo-EM Map-based Model Metrics Challenge sponsored by EMDataResource (&lt;a href="http://www.emdataresource.org"&gt;www.emdataresource.org&lt;/a&gt;, &lt;a href="http://challenges.emdataresource.org"&gt;challenges.emdataresource.org&lt;/a&gt;, &lt;a href="http://model-compare.emdataresource.org"&gt;model-compare.emdataresource.org&lt;/a&gt;). The goals of this challenge were (1) to assess the quality of models that can be produced using current modeling software, (2) to check the reproducibility of modeling results from different software developers and users, and (3) compare the performance of current metrics used for evaluation of models. The focus was on near-atomic resolution maps with an innovative twist: three of four target maps formed a resolution series (1.8 to 3.1 &amp;Aring;) from the same specimen and imaging experiment. Tools developed in previous challenges were expanded for managing, visualizing and analyzing the 63 submitted coordinate models, and several new metrics were introduced.&lt;/p&gt;

&lt;p&gt;File Descriptions:&lt;/p&gt;

&lt;ul&gt;
	&lt;li&gt;2019-EMDataResource-Challenge-web.pdf: Archive of News, Goals, Timeline, Targets, Modelling Instructions, Process, FAQ, Submission Instructions, Submission Summary Statistics source from the &lt;a href="https://challenges.emdataresource.org"&gt;EMDR Challenges&lt;/a&gt; website&lt;/li&gt;
	&lt;li&gt;correlation-images.tar.gz: Pairwise correlation tables for selected metric scores from the &lt;a href="https://model-compare.emdataresource.org"&gt;EMDR Model Compare&lt;/a&gt; website&lt;/li&gt;
	&lt;li&gt;maps.tar.gz: The maps used for Fit-to-Map analyses in the Challenge&lt;/li&gt;
	&lt;li&gt;models.tar.gz: The 63 models submitted by the modelling teams&lt;/li&gt;
	&lt;li&gt;results.tar.gz: The output logs for all of the analysis methods&lt;/li&gt;
	&lt;li&gt;Scores.xlsx: Scores for each model and analysis method, compiled into spreadsheet format&lt;/li&gt;
	&lt;li&gt;targets.tar.gz: The reference models used in the analysis&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;Post submission correction to the web archive PDF document: The full list of EMDataResource members on the model committee is as follows: Cathy Lawson, Andriy Kryshtafovych, Greg Pintilie, Mike Schmid, Helen Berman, Wah Chiu.&lt;/p&gt;</description>
    <description descriptionType="Other">EMDataResource is supported by the US National Institutes of Health (NIH)/National Institute of General Medical Science, R01GM079429.
The following additional grants are acknowledged for participant support. 
JSR and CW: NIH/ R35GM131883.
PDA, PVA, L-WH, JSR, TCT and CW: NIH/P01GM063210.
AS: National Science Foundation (NSF)/MCB-1942763 (CAREER), NIH/R01GM095583. The Singharoy team used supercomputing resources of the OLCF at the Oak Ridge National Laboratory, which is supported by the Office of Science at DOE under Contract No. DE-AC05-00OR22725.
DKihara: NIH/R01GM123055, NIH/R01GM133840, NSF/DMS1614777, NSF/CMMI1825941, NSF/MCB1925643, NSF/DBI2003635, Purdue Institute of Drug Discovery.
JSF: NIH/R01GM123159.
MI: Max Planck Society German Research Foundation/IG 109/1-1.
ACV: Max Planck Society German Research Foundation /FOR-1805.
DKumar: NIH/R37AI36040 and Welch Foundation/Q1279 (PI: BVV Prasad).
DS: NSF/DBI2030381.
TB, CMP, MW: Medical Research Council MR/N009614/1.
APJ, MW: Wellcome Trust 208398/Z/17/Z.
KC: Biotechnology and Biological Sciences Research Council BB/P000517/1.
MW: Biotechnology and Biological Sciences Research Council BB/P000975/1.</description>
  </descriptions>
</resource>
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