Evidence map›Paper›PMID 30114512›Full record

ArticleJournal of structural biology2018

The first single particle analysis Map Challenge: A summary of the assessments.

J Bernard Heymann, Roberto Marabini, Mohsen Kazemi, Carlos Oscar S Sorzano, Maya Holmdahl, Joshua H Mendez, Scott M Stagg, Slavica Jonic, Eugene Palovcak, Jean-Paul Armache and 6 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Journal of structural biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.

0numbers the graph read from it
0cells of the map it votes in
13citing papers in PubMed
–field-weighted citation impact
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

13 citing papers in PubMed.

  1. Article
  2. Article
  3. Review
  4. Article
  5. Article
  6. Article
  7. High resolution single particle Cryo-EM refinement using JSPR.Progress in biophysics and molecular biology · 2021
    Review
  8. Article
  9. Automatic local resolution-based sharpening of cryo-EM maps.Bioinformatics (Oxford, England) · 2020
    Article
  10. Review
  11. Evolving data standards for cryo-EM structures.Structural dynamics (Melville, N.Y.) · 2020
    Article
  12. Single-particle reconstruction statistics: a diagnostic tool in solving biomolecular structures by cryo-EM.Acta crystallographica. Section F, Structural biology communications · 2019
    Review
  13. Comparing cryo-EM structures.Journal of structural biology · 2018
    Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

16 authors.

J Bernard HeymannLaboratory for Structural Biology Research, National Institute of Arthritis, Musculoskeletal and Skin Diseases, NIH, Bethesda, MD 20892, USA. Electronic address: bernard_heymann@nih.gov.
Roberto MarabiniEscuela Politécnica Superior, Universidad Autónoma de Madrid, 28049 Cantoblanco, Madrid, Spain.
Mohsen KazemiDepartment of Biochemistry and Molecular Biology, School of Biomedical Sciences, The University of Melbourne, VIC 3010, Australia; Biocomputing Unit, National Center for Biotechnology (CSIC), C/Darwin, 3, Campus Universidad Autónoma, 28049 Cantoblanco, Madrid, Spain.
Carlos Oscar S SorzanoBiocomputing Unit, National Center for Biotechnology (CSIC), C/Darwin, 3, Campus Universidad Autónoma, 28049 Cantoblanco, Madrid, Spain.
Maya HolmdahlEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD England, United Kingdom.
Joshua H MendezDepartment of Physics, Florida State University, 77 Chieftan Way, Tallahassee, FL 32306, USA.
Scott M StaggInstitute of Molecular Biophysics, Florida State University, 91 Chieftan Way, Tallahassee, FL 32306-4380, USA; Department of Chemistry and Biochemistry, Florida State University, 95 Chieftain Way, Tallahassee, FL 32306, USA.
Slavica JonicSorbonne Université, UMR CNRS 7590, Muséum National d'Histoire Naturelle, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, 75005 Paris, France.
Eugene PalovcakDepartment of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
Jean-Paul ArmacheDepartment of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
Jianhua ZhaoDepartment of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
Yifan ChengDepartment of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA.
Grigore PintilieDepartment of Bioengineering, Stanford University, Stanford, CA, 94305 USA.
Wah ChiuDepartment of Bioengineering, Stanford University, Stanford, CA, 94305 USA.
Ardan PatwardhanEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD England, United Kingdom.
Jose-Maria CarazoBiocomputing Unit, National Center for Biotechnology (CSIC), C/Darwin, 3, Campus Universidad Autónoma, 28049 Cantoblanco, Madrid, Spain.

Funding

3 D ELECTRON MICROSCOPY OF MACROMOLECULES (5P41RR002250-27)P41GM103832 · NIGMS · STANFORD UNIVERSITY · PI CHIU, WAH · 2012 to 2019
$15.1M
Unified Data Resource for Large Complexes Determined by Cryo-Electron MicroscopyR01GM079429 · NIGMS · STANFORD UNIVERSITY · PI CHIU, WAH · 2007 to 2021
$11.6M
STRUCTURAL BIOLOGY TRAINING PROGRAMT32GM008284 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI KORTEMME, TANJA · 1988 to 2022
$10.1M
Tools For High-Throughput High-Resolution Three Dimensional Electron MicroscopyR01GM108753 · NIGMS · FLORIDA STATE UNIVERSITY · PI STAGG, SCOTT M · 2015 to 2020
$1.6M
Howard Hughes Medical InstituteIntramural NIH HHS Z99 AR999999NIGMS NIH HHS P41 GM103832NIGMS NIH HHS R01 GM079429NIGMS NIH HHS R01 GM108753NIGMS NIH HHS T32 GM008284
6 · The paper itself

Abstract

The recent successes of cryo-electron microscopy fostered great expectation of solving many new and previously recalcitrant biomolecular structures. However, it also brings with it the danger of compromising the validity of the outcomes if not done properly. The Map Challenge is a first step in assessing the state of the art and to shape future developments in data processing. The organizers presented seven cases for single particle reconstruction, and 27 members of the community responded with 66 submissions. Seven groups analyzed these submissions, resulting in several assessment reports, summarized here. We devised a range of analyses to evaluate the submitted maps, including visual impressions, Fourier shell correlation, pairwise similarity and interpretation through modeling. Unfortunately, we did not find strong trends. We ascribe this to the complexity of the challenge, dealing with multiple cases, software packages and processing approaches. This puts the user in the spotlight, where his/her choices becomes the determinant of map quality. The future focus should therefore be on promulgating best practices and encapsulating these in the software. Such practices include adherence to validation principles, most notably the processing of independent sets, proper resolution-limited alignment, appropriate masking and map sharpening. We consider the Map Challenge to be a highly valuable exercise that should be repeated frequently or on an ongoing basis.

Indexed as

AlgorithmsCryoelectron MicroscopyImage Processing, Computer-AssistedImaging, Three-DimensionalProtein ConformationSoftwareCryo-electron microscopyFourier shell correlationPower spectraReconstructionResolutionSingle particle analysisValidation

Identifiers

PMID30114512
PMCPMC6205511

What OpenQuestion holds

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Read underepoch 390

Registered trials

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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.