Evidence map›Paper›PMID 27633552›Full record

ArticleNature communications2016

Determining crystal structures through crowdsourcing and coursework.

Scott Horowitz, Brian Koepnick, Raoul Martin, Agnes Tymieniecki, Amanda A Winburn, Seth Cooper, Jeff Flatten, David S Rogawski, Nicole M Koropatkin, Tsinatkeab T Hailu and 14 more

Erratum issuedOpen access · goldAbstract read
In one paragraph

Article in Nature communications, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 17 papers.

0numbers the graph read from it
0cells of the map it votes in
17citing papers in PubMed
6.6field-weighted citation impact, top 3% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

17 citing papers in PubMed, 79 citations in OpenAlex.

  1. Article
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  4. The N-Acetylglucosamine Kinase fromInternational journal of molecular sciences · 2021
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  7. Review
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  10. Scientific Discovery Games for Biomedical Research.Annual review of biomedical data science · 2019
    Article
  11. Article
  12. Article
  13. Repurposing Citizen Science Games as Software Tools for Professional Scientists.FDG : proceedings of the International Conference on Foundations of Digital Games. International Conference on the Foundations of Digital Games · 2018
    Article
  14. Article
  15. Crowd sourcing difficult problems in protein scienceProtein science : a publication of the Protein Society · 2017
    Review
  16. Article
  17. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

24 authors at 7 institutions in 3 countries.

Scott HorowitzDepartment of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA.
Brian KoepnickDepartment of Biochemistry, University of Washington, Seattle, Washington 98195, USA.
Raoul MartinDepartment of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA.
Agnes TymienieckiDepartment of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA.
Amanda A WinburnCenter for Complex Networks and Systems Research, Department of Informatics, Indiana University, Bloomington, Indiana 47408, USA.ORCID 0000-0001-6579-1120
Seth CooperNortheastern University, College of Computer and Information Science, Boston, Massachusetts 02115, USA.
Jeff FlattenDepartment of Computer Science and Engineering, Center for Game Science, University of Washington, Seattle, Washington 98195, USA.
David S RogawskiDepartment of Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA.
Nicole M KoropatkinDepartment of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan 48109, USA.
Tsinatkeab T HailuDepartment of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA.
Neha JainDepartment of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA.
Philipp KoldeweyDepartment of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA.
Logan S AhlstromDepartment of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA.
Matthew R ChapmanDepartment of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA.
Andrew P SikkemaDepartment of Biological Chemistry and Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, USA.
Meredith A SkibaDepartment of Biological Chemistry and Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, USA.
Finn P MaloneyChemical Biology Doctoral Program, University of Michigan, Ann Arbor, Michigan 48109, USA.
Felix R M BeinlichDepartment of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA.
Foldit Players
University of Michigan students
Zoran PopovićDepartment of Computer Science and Engineering, Center for Game Science, University of Washington, Seattle, Washington 98195, USA.
David BakerDepartment of Biochemistry, University of Washington, Seattle, Washington 98195, USA.
Firas KhatibDepartment of Computer and Information Science, University of Massachusetts Dartmouth, Dartmouth, Massachusetts 02747, USA.
James C A BardwellDepartment of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA.
University of Washington · USUniversity of Michigan · USHoward Hughes Medical Institute · USUniversity of Massachusetts Dartmouth · USForschungszentrum Jülich · DEIndiana University Bloomington · USNortheastern University · US

Funding

MICHIGAN MEDICAL SCIENTIST TRAINING PROGRAMT32GM007863 · NIGMS · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI COLLINS, KATHLEEN L. · 1985 to 2024
$38.3M
Cellular Biotechnology Training Program (CBTP)T32GM008353 · NIGMS · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI SCHWENDEMAN, ANNA · 1991 to 2021
$9.3M
MICHIGAN CHEMISTRY-BIOLOGY INTERFACE TRAINING PROGRAMT32GM008597 · NIGMS · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI MONTGOMERY, JOHN · 1996 to 2018
$5.0M
MICHIGAN MOLECULAR BIOPHYSICS TRAINING PROGRAMT32GM008270 · NIGMS · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI BROOKS, CHARLES L · 1988 to 2012
$4.5M
Protein and Chemical Modulation of Curli Amyloid BiogenesisR01GM118651 · NIGMS · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI Matthew Richard Chapman · 2016 to 2026
$3.0M
Mechanism of an Acid Activated ChaperoneR01GM102829 · NIGMS · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI BARDWELL, JAMES, JAKOB, URSULA H. · 2013 to 2016
$1.8M
NIGMS NIH HHS R01 GM102829NIGMS NIH HHS R01 GM118651NIGMS NIH HHS T32 GM007863NIGMS NIH HHS T32 GM008270NIGMS NIH HHS T32 GM008353NIGMS NIH HHS T32 GM008597
6 · The paper itself

Abstract

We show here that computer game players can build high-quality crystal structures. Introduction of a new feature into the computer game Foldit allows players to build and real-space refine structures into electron density maps. To assess the usefulness of this feature, we held a crystallographic model-building competition between trained crystallographers, undergraduate students, Foldit players and automatic model-building algorithms. After removal of disordered residues, a team of Foldit players achieved the most accurate structure. Analysing the target protein of the competition, YPL067C, uncovered a new family of histidine triad proteins apparently involved in the prevention of amyloid toxicity. From this study, we conclude that crystallographers can utilize crowdsourcing to interpret electron density information and to produce structure solutions of the highest quality.

Indexed as

CurriculumModels, ChemicalSoftwareCrowdsourcingCrystallographyHydrolasesProtein Conformationhistidine triad proteinHydrolases

Identifiers

PMID27633552
PMCPMC5028414
OpenAlexW2519080286

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.