Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
High-resolution single-particle orientation refinement based on spectrally self-adapting common lines
KTH, School of Technology and Health (STH), Structural Biotechnology.
KTH, School of Technology and Health (STH), Structural Biotechnology.
2009 (English)In: Journal of Structural Biology, ISSN 1047-8477, E-ISSN 1095-8657, Vol. 167, no 1, 83-94 p.Article in journal (Refereed) Published
Abstract [en]

Three-dimensional (3D) structure determination from electron microscopic images of single molecules can be difficult for particles with low or no internal symmetry, and for images with low signal-to-noise ratio (SNR), due to the existence of false maxima in the scoring function used for orientation search. In attempt to improve robustness of orientation parameter refinement towards noise and poor starting reconstruction quality, we have developed a method for common lines-based orientation search in Fourier space. The Fourier-space formulation enables inclusion of resolution (spatial frequency of the low-pass limit) as a variable that is adjusted in a particle-dependent, self-adaptive manner. The method allows for the underlying 3D structure to be estimated to high resolution, and requires only a crude, low-resolution reconstruction as starting-point for refinement. Benchmarking of the method is performed on experimental and synthetic data.

Place, publisher, year, edition, pages
2009. Vol. 167, no 1, 83-94 p.
Keyword [en]
Electron microscopy, Single-particle, Refinement, Correlation coefficient, Common line
National Category
Biochemistry and Molecular Biology
Identifiers
URN: urn:nbn:se:kth:diva-27333DOI: 10.1016/j.jsb.2009.04.009ISI: 000266819300011PubMedID: 19410651OAI: oai:DiVA.org:kth-27333DiVA: diva2:376068
Note
QC 20101210Available from: 2010-12-09 Created: 2010-12-09 Last updated: 2017-12-11Bibliographically approved
In thesis
1. Towards unbiased 3D reconstruction: in single-particle cryo-electron microscopy
Open this publication in new window or tab >>Towards unbiased 3D reconstruction: in single-particle cryo-electron microscopy
2010 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Cryo-electron microscopy of freestanding molecules (single-particles) plays a pivotal role in the difficult and pressing challenge of determining the structures of large macromolecular complexes. Molecular volumes are generated by aligning large sets of randomly oriented two-dimensional (2D) projection images in three dimensions (3D) before reconstruction is performed using tomographic techniques. The increasing popularity of the single-particle method is highly correlated with technical advances in instrumentation and computation. This thesis introduces new computational methods for 3D structure determination from electron microscopic projection images of single molecules. The algorithms have been developed to fill a gap in the single particle methodology – the lack of methods for ab initio 3D reconstruction of asymmetrical or low-symmetry molecules co-existing in different functional states. The proposed approach does not rely on a priori information about the structure or the character of the sample heterogeneity, which minimizes template dependence and makes the methods applicable to a wide range of single molecules. The presented algorithms constitute the basis of a new open source software package - SIMPLE (Single-particle IMage Processing Linux Engine). SIMPLE is an efficient and easy-to-use image processing system for semi-automated ab initio 3D reconstruction from challenging single-particle data sets (asymmetrical particles, significant degree of heterogeneity).

Place, publisher, year, edition, pages
Stockholm: KTH, 2010. 38 p.
Series
Trita-STH : report, ISSN 1653-3836 ; 2010:7
National Category
Industrial Biotechnology
Identifiers
urn:nbn:se:kth:diva-27612 (URN)978-91-7415-837-3 (ISBN)
Public defence
2011-01-14, Föreläsningssalen, Novum, Hälsovägen 7, Huddinge, 10:00 (English)
Opponent
Supervisors
Note
QC 20101214Available from: 2010-12-14 Created: 2010-12-14 Last updated: 2010-12-16Bibliographically approved

Open Access in DiVA

No full text

Other links

Publisher's full textPubMed

Search in DiVA

By author/editor
Elmlund, DominikaElmlund, Hans
By organisation
Structural Biotechnology
In the same journal
Journal of Structural Biology
Biochemistry and Molecular Biology

Search outside of DiVA

GoogleGoogle Scholar

doi
pubmed
urn-nbn

Altmetric score

doi
pubmed
urn-nbn
Total: 48 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf