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2024-01-04T07:47:45Z

Created page with "== Citation == Chaillet, Marten L. / van der Schot, Gijs / Gubins, Ilja / Roet, Sander / Veltkamp, Remco C. / Förster, Friedrich. Extensive angular sampling enables the sens..."

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== Citation ==

Chaillet, Marten L. / van der Schot, Gijs / Gubins, Ilja / Roet, Sander / Veltkamp, Remco C. / Förster, Friedrich. Extensive angular sampling enables the sensitive localization of macromolecules in electron tomograms. 2023. Intl. J. of Molecular Sciences, Vol. 24, No. 17, p. 13375

== Abstract ==

Cryo-electron tomography provides 3D images of macromolecules in their cellular context.
To detect macromolecules in tomograms, template matching (TM) is often used, which uses 3D
models that are often reliable for substantial parts of the macromolecules. However, the extent of
rotational searches in particle detection has not been investigated due to computational limitations.
Here, we provide a GPU implementation of TM as part of the PyTOM software package, which
drastically speeds up the orientational search and allows for sampling beyond the Crowther criterion
within a feasible timeframe. We quantify the improvements in sensitivity and false-discovery rate
for the examples of ribosome identification and detection. Sampling at the Crowther criterion,
which was effectively impossible with CPU implementations due to the extensive computation times,
allows for automated extraction with high sensitivity. Consequently, we also show that an extensive
angular sample renders 3D TM sensitive to the local alignment of tilt series and damage induced by
focused ion beam milling. With this new release of PyTOM, we focused on integration with other
software packages that support more refined subtomogram-averaging workflows. The automated
classification of ribosomes by TM with appropriate angular sampling on locally corrected tomograms
has a sufficiently low false-discovery rate, allowing for it to be directly used for high-resolution
averaging and adequate sensitivity to reveal polysome organization.

== Keywords ==

== Links ==

https://www.mdpi.com/1422-0067/24/17/13375

== Related software ==

== Related methods ==

== Comments ==

2023Chaillet Extensive - Revision history

WikiSysop: Created page with "== Citation == Chaillet, Marten L. / van der Schot, Gijs / Gubins, Ilja / Roet, Sander / Veltkamp, Remco C. / Förster, Friedrich. Extensive angular sampling enables the sens..."