Format

Send to

Choose Destination
J Struct Biol. 2018 Nov;204(2):291-300. doi: 10.1016/j.jsb.2018.08.010. Epub 2018 Aug 13.

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

Author information

1
Laboratory for Structural Biology Research, National Institute of Arthritis, Musculoskeletal and Skin Diseases, NIH, Bethesda, MD 20892, USA. Electronic address: bernard_heymann@nih.gov.
2
Escuela Politécnica Superior, Universidad Autónoma de Madrid, 28049 Cantoblanco, Madrid, Spain.
3
Department 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.
4
Biocomputing Unit, National Center for Biotechnology (CSIC), C/Darwin, 3, Campus Universidad Autónoma, 28049 Cantoblanco, Madrid, Spain.
5
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD England, United Kingdom.
6
Department of Physics, Florida State University, 77 Chieftan Way, Tallahassee, FL 32306, USA.
7
Institute 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.
8
Sorbonne Université, UMR CNRS 7590, Muséum National d'Histoire Naturelle, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, 75005 Paris, France.
9
Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
10
Department 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.
11
Department of Bioengineering, Stanford University, Stanford, CA, 94305 USA.

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.

KEYWORDS:

Cryo-electron microscopy; Fourier shell correlation; Power spectra; Reconstruction; Resolution; Single particle analysis; Validation

PMID:
30114512
PMCID:
PMC6205511
[Available on 2019-11-01]
DOI:
10.1016/j.jsb.2018.08.010

Supplemental Content

Full text links

Icon for Elsevier Science
Loading ...
Support Center