WikiSysop: Created page with "== Citation == Selvaraj, J., Wang, L. and Cheng, J. 2025. CryoTEN: efficiently enhancing cryo-EM density maps using transformers. Bioinformatics. 41, 3 (2025), btaf092. == Abstract == Motivation: Cryogenic Electron Microscopy (cryo-EM) is a core experimental technique used to determine the structure of macromolecules such as proteins. However, the effectiveness of cryo-EM is often hindered by the noise and missing density values in cryo-EM density maps caused by exper..."

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Created page with "== Citation == Selvaraj, J., Wang, L. and Cheng, J. 2025. CryoTEN: efficiently enhancing cryo-EM density maps using transformers. Bioinformatics. 41, 3 (2025), btaf092. == Abstract == Motivation: Cryogenic Electron Microscopy (cryo-EM) is a core experimental technique used to determine the structure of macromolecules such as proteins. However, the effectiveness of cryo-EM is often hindered by the noise and missing density values in cryo-EM density maps caused by exper..."

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== Citation ==

Selvaraj, J., Wang, L. and Cheng, J. 2025. CryoTEN: efficiently enhancing cryo-EM density maps using transformers. Bioinformatics. 41, 3 (2025), btaf092.

== Abstract ==

Motivation: Cryogenic Electron Microscopy (cryo-EM) is a core experimental technique used to determine the structure
of macromolecules such as proteins. However, the effectiveness of cryo-EM is often hindered by the noise and missing
density values in cryo-EM density maps caused by experimental conditions such as low contrast and conformational
heterogeneity. Although various global and local map sharpening techniques are widely employed to improve cryo-EM
density maps, it is still challenging to efficiently improve their quality for building better protein structures from them.
Results: In this study, we introduce CryoTEN - a three-dimensional U-Net style transformer to improve cryo-EM maps
effectively. CryoTEN is trained using a diverse set of 1,295 cryo-EM maps as inputs and their corresponding simulated
maps generated from known protein structures as targets. An independent test set containing 150 maps is used to evaluate
CryoTEN, and the results demonstrate that it can robustly enhance the quality of cryo-EM density maps. In addition, the
automatic de novo protein structure modeling shows that the protein structures built from the density maps processed
by CryoTEN have substantially better quality than those built from the original maps. Compared to the existing stateof-
the-art deep learning methods for enhancing cryo-EM density maps, CryoTEN ranks second in improving the quality
of density maps, while running > 10 times faster and requiring much less GPU memory than them.
Availability and implementation: The source code and data is freely available at https://github.com/
jianlin-cheng/cryoten

== Keywords ==

== Links ==

https://academic.oup.com/bioinformatics/article/41/3/btaf092/8045306

== Related software ==

== Related methods ==

== Comments ==

2025Selvaraj CryoTEN - Revision history