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


JSON-LD (schema.org) Export

{
  "inLanguage": {
    "alternateName": "eng", 
    "@type": "Language", 
    "name": "English"
  }, 
  "description": "<p>This is the full dataset of the 2019 Cryo-EM Map-based Model Metrics Challenge sponsored by EMDataResource (<a href=\"http://www.emdataresource.org\">www.emdataresource.org</a>, <a href=\"http://challenges.emdataresource.org\">challenges.emdataresource.org</a>, <a href=\"http://model-compare.emdataresource.org\">model-compare.emdataresource.org</a>). 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 &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.</p>\n\n<p>File Descriptions:</p>\n\n<ul>\n\t<li>2019-EMDataResource-Challenge-web.pdf: Archive of News, Goals, Timeline, Targets, Modelling Instructions, Process, FAQ, Submission Instructions, Submission Summary Statistics source from the <a href=\"https://challenges.emdataresource.org\">EMDR Challenges</a> website</li>\n\t<li>correlation-images.tar.gz: Pairwise correlation tables for selected metric scores from the <a href=\"https://model-compare.emdataresource.org\">EMDR Model Compare</a> website</li>\n\t<li>maps.tar.gz: The maps used for Fit-to-Map analyses in the Challenge</li>\n\t<li>models.tar.gz: The 63 models submitted by the modelling teams</li>\n\t<li>results.tar.gz: The output logs for all of the analysis methods</li>\n\t<li>Scores.xlsx: Scores for each model and analysis method, compiled into spreadsheet format</li>\n\t<li>targets.tar.gz: The reference models used in the analysis</li>\n</ul>\n\n<p>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.</p>", 
  "license": "https://creativecommons.org/licenses/by/4.0/legalcode", 
  "creator": [
    {
      "affiliation": "Rutgers University", 
      "@id": "https://orcid.org/0000-0002-3261-7035", 
      "@type": "Person", 
      "name": "Lawson, Catherine L"
    }, 
    {
      "affiliation": "University of California Davis", 
      "@id": "https://orcid.org/0000-0001-5066-7178", 
      "@type": "Person", 
      "name": "Kryshtafovych, Andriy"
    }, 
    {
      "affiliation": "Lawrence Berkeley Laboratory", 
      "@id": "https://orcid.org/0000-0001-9333-8219", 
      "@type": "Person", 
      "name": "Adams, Paul D"
    }, 
    {
      "affiliation": "Lawrence Berkeley Laboratory", 
      "@id": "https://orcid.org/0000-0002-5052-991X", 
      "@type": "Person", 
      "name": "Afonine, Pavel V"
    }, 
    {
      "affiliation": "University of Texas Health Science Center", 
      "@id": "https://orcid.org/0000-0001-9039-8523", 
      "@type": "Person", 
      "name": "Baker, Matthew L"
    }, 
    {
      "affiliation": "Scripps Research Institute, La Jolla", 
      "@id": "https://orcid.org/0000-0002-1016-862X", 
      "@type": "Person", 
      "name": "Barad, Benjamin A"
    }, 
    {
      "affiliation": "University of York", 
      "@id": "https://orcid.org/0000-0002-8465-4823", 
      "@type": "Person", 
      "name": "Bond, Paul"
    }, 
    {
      "affiliation": "UKRI Science and Technology Facilities Council", 
      "@id": "https://orcid.org/0000-0001-5307-348X", 
      "@type": "Person", 
      "name": "Burnley, Tom"
    }, 
    {
      "affiliation": "Pacific Lutheran University", 
      "@id": "https://orcid.org/0000-0002-8345-343X", 
      "@type": "Person", 
      "name": "Cao, Renzhi"
    }, 
    {
      "affiliation": "University of Missouri", 
      "@id": "https://orcid.org/0000-0003-0305-2853", 
      "@type": "Person", 
      "name": "Cheng, Jianlin"
    }, 
    {
      "affiliation": "European Molecular Biology Laboratory", 
      "@id": "https://orcid.org/0000-0002-3796-8352", 
      "@type": "Person", 
      "name": "Chojnowski, Grzegorz"
    }, 
    {
      "affiliation": "University of York", 
      "@id": "https://orcid.org/0000-0002-0189-1437", 
      "@type": "Person", 
      "name": "Cowtan, Kevin"
    }, 
    {
      "affiliation": "Stony Brook University", 
      "@id": "https://orcid.org/0000-0002-2390-2002", 
      "@type": "Person", 
      "name": "Dill, Ken"
    }, 
    {
      "affiliation": "University of Washington Seattle", 
      "@id": "https://orcid.org/0000-0002-7524-8938", 
      "@type": "Person", 
      "name": "DiMaio, Frank"
    }, 
    {
      "affiliation": "University of Washington Seattle", 
      "@id": "https://orcid.org/0000-0001-7024-7998", 
      "@type": "Person", 
      "name": "Farrell, Daniel P"
    }, 
    {
      "affiliation": "University of California San Francisco", 
      "@id": "https://orcid.org/0000-0002-5080-2859", 
      "@type": "Person", 
      "name": "Fraser, James S"
    }, 
    {
      "affiliation": "University of California San Diego", 
      "@id": "https://orcid.org/0000-0001-6653-6682", 
      "@type": "Person", 
      "name": "Herzik, Mark A Jr"
    }, 
    {
      "affiliation": "University of York", 
      "@id": "https://orcid.org/0000-0003-1039-8000", 
      "@type": "Person", 
      "name": "Hoh, Soon Wen"
    }, 
    {
      "affiliation": "Saint Louis University", 
      "@id": "https://orcid.org/0000-0002-8584-5154", 
      "@type": "Person", 
      "name": "Hou, Jie"
    }, 
    {
      "affiliation": "Los Alamos National Laboratory", 
      "@id": "https://orcid.org/0000-0001-6690-8458", 
      "@type": "Person", 
      "name": "Hung, Li-Wei"
    }, 
    {
      "affiliation": "Max Planck Institute for Biophysical Chemistry", 
      "@id": "https://orcid.org/0000-0001-8781-1604", 
      "@type": "Person", 
      "name": "Igaev, Maxim"
    }, 
    {
      "affiliation": "UKRI Science and Technology Facilities Council", 
      "@id": "https://orcid.org/0000-0002-0997-8422", 
      "@type": "Person", 
      "name": "Joseph, Agnel P"
    }, 
    {
      "affiliation": "Purdue University", 
      "@id": "https://orcid.org/0000-0003-4091-6614", 
      "@type": "Person", 
      "name": "Kihara, Daisuke"
    }, 
    {
      "affiliation": "Baylor College of Medicine", 
      "@id": "https://orcid.org/0000-0002-2721-678X", 
      "@type": "Person", 
      "name": "Kumar, Dilip"
    }, 
    {
      "affiliation": "Arizona State University", 
      "@type": "Person", 
      "name": "Mittal, Sumit"
    }, 
    {
      "affiliation": "University of California Davis", 
      "@id": "https://orcid.org/0000-0002-4803-0378", 
      "@type": "Person", 
      "name": "Monastryrskyy, Bohdan"
    }, 
    {
      "affiliation": "University of York", 
      "@id": "https://orcid.org/0000-0002-6347-9587", 
      "@type": "Person", 
      "name": "Olek, Mateusz"
    }, 
    {
      "affiliation": "UKRI Science and Technology Facilities Council", 
      "@id": "https://orcid.org/0000-0002-4883-1546", 
      "@type": "Person", 
      "name": "Palmer, Colin M"
    }, 
    {
      "affiliation": "European Bioinformatics Institute", 
      "@id": "https://orcid.org/0000-0001-7663-9028", 
      "@type": "Person", 
      "name": "Patwardhan, Ardan"
    }, 
    {
      "affiliation": "University of Florida", 
      "@id": "https://orcid.org/0000-0002-5054-5338", 
      "@type": "Person", 
      "name": "Perez, Alberto"
    }, 
    {
      "affiliation": "University of Washington Bothell", 
      "@id": "https://orcid.org/0000-0002-8285-571X", 
      "@type": "Person", 
      "name": "Pfab, Jonas"
    }, 
    {
      "affiliation": "Stanford University", 
      "@id": "https://orcid.org/0000-0002-0848-5335", 
      "@type": "Person", 
      "name": "Pintilie, Greg D"
    }, 
    {
      "affiliation": "Duke University", 
      "@id": "https://orcid.org/0000-0002-3311-2944", 
      "@type": "Person", 
      "name": "Richardson, Jane S"
    }, 
    {
      "affiliation": "Purdue University", 
      "@id": "https://orcid.org/0000-0002-4167-2108", 
      "@type": "Person", 
      "name": "Sarkar, Daipayan"
    }, 
    {
      "affiliation": "Forschungszentrum J\u00fclich", 
      "@id": "https://orcid.org/0000-0002-8481-6298", 
      "@type": "Person", 
      "name": "Sch\u00e4fer, Luisa U"
    }, 
    {
      "affiliation": "Stanford University", 
      "@id": "https://orcid.org/0000-0003-1077-5750", 
      "@type": "Person", 
      "name": "Schmid, Michael F"
    }, 
    {
      "affiliation": "Heinrich Heine University D\u00fcsseldorf", 
      "@id": "https://orcid.org/0000-0003-1803-5431", 
      "@type": "Person", 
      "name": "Schr\u00f6der, Gunnar F"
    }, 
    {
      "affiliation": "Broad Institute of MIT and Harvard", 
      "@type": "Person", 
      "name": "Shekhar, Mrinal"
    }, 
    {
      "affiliation": "University of Washington Bothell", 
      "@id": "https://orcid.org/0000-0001-7039-2589", 
      "@type": "Person", 
      "name": "Si, Dong"
    }, 
    {
      "affiliation": "Arizona State University", 
      "@id": "https://orcid.org/0000-0002-9000-2397", 
      "@type": "Person", 
      "name": "Singharoy, Abishek"
    }, 
    {
      "affiliation": "Purdue University", 
      "@id": "https://orcid.org/0000-0002-5339-909X", 
      "@type": "Person", 
      "name": "Terashi, Genki"
    }, 
    {
      "affiliation": "New Mexico Consortium", 
      "@id": "https://orcid.org/0000-0001-6384-0320", 
      "@type": "Person", 
      "name": "Terwilliger, Thomas C"
    }, 
    {
      "affiliation": "Max Planck Institute for Biophysical Chemistry", 
      "@id": "https://orcid.org/0000-0002-8865-0651", 
      "@type": "Person", 
      "name": "Vaiana, Andrea"
    }, 
    {
      "affiliation": "University of Washington Seattle", 
      "@id": "https://orcid.org/0000-0002-7095-5983", 
      "@type": "Person", 
      "name": "Wang, Liguo"
    }, 
    {
      "affiliation": "University of California San Francisco", 
      "@id": "https://orcid.org/0000-0002-4225-7459", 
      "@type": "Person", 
      "name": "Wankowicz, Stephanie A"
    }, 
    {
      "affiliation": "Duke University", 
      "@id": "https://orcid.org/0000-0002-5808-8768", 
      "@type": "Person", 
      "name": "Williams, Christopher J"
    }, 
    {
      "affiliation": "UKRI Science and Technology Facilities Council", 
      "@id": "https://orcid.org/0000-0003-0496-6796", 
      "@type": "Person", 
      "name": "Winn, Martyn"
    }, 
    {
      "affiliation": "University of Missouri", 
      "@id": "https://orcid.org/0000-0002-1545-3462", 
      "@type": "Person", 
      "name": "Wu, Tianqi"
    }, 
    {
      "affiliation": "Janssen Research and Development", 
      "@id": "https://orcid.org/0000-0001-7520-0646", 
      "@type": "Person", 
      "name": "Yu, Xiaodi"
    }, 
    {
      "affiliation": "Stanford University", 
      "@id": "https://orcid.org/0000-0003-0414-4776", 
      "@type": "Person", 
      "name": "Zhang, Kaiming"
    }, 
    {
      "affiliation": "Rutgers University", 
      "@id": "https://orcid.org/0000-0002-3337-0660", 
      "@type": "Person", 
      "name": "Berman, Helen M"
    }, 
    {
      "affiliation": "Stanford University", 
      "@id": "https://orcid.org/0000-0002-8910-3078", 
      "@type": "Person", 
      "name": "Chiu, Wah"
    }
  ], 
  "url": "https://zenodo.org/record/4148789", 
  "datePublished": "2020-10-28", 
  "keywords": [
    "cryo-EM", 
    "model validation", 
    "3D structure"
  ], 
  "@context": "https://schema.org/", 
  "distribution": [
    {
      "contentUrl": "https://www.zenodo.org/api/files/1c53598b-95e9-4e79-8f05-cfb42a3a2b0c/2019-EMDataResource-Challenge-web.pdf", 
      "encodingFormat": "pdf", 
      "@type": "DataDownload"
    }, 
    {
      "contentUrl": "https://www.zenodo.org/api/files/1c53598b-95e9-4e79-8f05-cfb42a3a2b0c/correlation-images.tar.gz", 
      "encodingFormat": "gz", 
      "@type": "DataDownload"
    }, 
    {
      "contentUrl": "https://www.zenodo.org/api/files/1c53598b-95e9-4e79-8f05-cfb42a3a2b0c/maps.tar.gz", 
      "encodingFormat": "gz", 
      "@type": "DataDownload"
    }, 
    {
      "contentUrl": "https://www.zenodo.org/api/files/1c53598b-95e9-4e79-8f05-cfb42a3a2b0c/models.tar.gz", 
      "encodingFormat": "gz", 
      "@type": "DataDownload"
    }, 
    {
      "contentUrl": "https://www.zenodo.org/api/files/1c53598b-95e9-4e79-8f05-cfb42a3a2b0c/results.tar.gz", 
      "encodingFormat": "gz", 
      "@type": "DataDownload"
    }, 
    {
      "contentUrl": "https://www.zenodo.org/api/files/1c53598b-95e9-4e79-8f05-cfb42a3a2b0c/Scores.xlsx", 
      "encodingFormat": "xlsx", 
      "@type": "DataDownload"
    }, 
    {
      "contentUrl": "https://www.zenodo.org/api/files/1c53598b-95e9-4e79-8f05-cfb42a3a2b0c/targets.tar.gz", 
      "encodingFormat": "gz", 
      "@type": "DataDownload"
    }
  ], 
  "identifier": "https://doi.org/10.5281/zenodo.4148789", 
  "@id": "https://doi.org/10.5281/zenodo.4148789", 
  "@type": "Dataset", 
  "name": "2019 EMDataResource Model Metrics Challenge Dataset"
}
290
177
views
downloads
All versions This version
Views 290290
Downloads 177177
Data volume 2.0 GB2.0 GB
Unique views 258258
Unique downloads 136136

Share

Cite as