Evidence map›Paper›PMID 28989723›Full record

ArticleIUCrJ2017

Single-particle cryo-EM using alignment by classification (ABC): the structure of

Pavel Afanasyev, Charlotte Seer-Linnemayr, Raimond B G Ravelli, Rishi Matadeen, Sacha De Carlo, Bart Alewijnse, Rodrigo V Portugal, Navraj S Pannu, Michael Schatz, Marin van Heel

Abstract read
In one paragraph

Article in IUCrJ, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.

0numbers the graph read from it
0cells of the map it votes in
14citing 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

14 citing papers in PubMed.

  1. Rescaling FSC curves.Acta crystallographica. Section D, Structural biology · 2025
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  11. Review
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  13. New tools for the analysis and validation of cryo-EM maps and atomic models.Acta crystallographica. Section D, Structural biology · 2018
    Article
  14. 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

10 authors.

Pavel AfanasyevInstitute of Biology Leiden, Leiden University, 2333 CC Leiden, The Netherlands.ORCID https://orcid.org/0000-0002-6353-6895
Charlotte Seer-LinnemayrInstitute of Molecular Biology, University of Zurich, Switzerland.
Raimond B G RavelliInstitute of Nanoscopy, Maastricht University, 6211 LK Maastricht, The Netherlands.
Rishi MatadeenNetherlands Centre for Electron Nanoscopy (NeCEN), Einsteinweg 55, 2333 CC Leiden, The Netherlands.
Sacha De CarloNetherlands Centre for Electron Nanoscopy (NeCEN), Einsteinweg 55, 2333 CC Leiden, The Netherlands.
Bart AlewijnseInstitute of Biology Leiden, Leiden University, 2333 CC Leiden, The Netherlands.
Rodrigo V PortugalBrazilian Nanotechnology National Laboratory (LNNANO), Campinas, SP, Brazil.
Navraj S PannuLeiden Institute of Chemistry, Leiden University, 2333 CC Leiden, The Netherlands.
Michael SchatzImage Science Software GmbH, 14193 Berlin, Germany.
Marin van HeelInstitute of Biology Leiden, Leiden University, 2333 CC Leiden, The Netherlands.

Funding

Biotechnology and Biological Sciences Research Council BB/G015236/1
6 · The paper itself

Abstract

Single-particle cryogenic electron microscopy (cryo-EM) can now yield near-atomic resolution structures of biological complexes. However, the reference-based alignment algorithms commonly used in cryo-EM suffer from reference bias, limiting their applicability (also known as the 'Einstein from random noise' problem). Low-dose cryo-EM therefore requires robust and objective approaches to reveal the structural information contained in the extremely noisy data, especially when dealing with small structures. A reference-free pipeline is presented for obtaining near-atomic resolution three-dimensional reconstructions from heterogeneous ('four-dimensional') cryo-EM data sets. The methodologies integrated in this pipeline include

Indexed as

alignment by classificationangular reconstitutioncryo-EMMSAworm haemoglobin

Identifiers

PMID28989723
PMCPMC5619859

What OpenQuestion holds

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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.