RT Journal Article
SR Electronic
T1 CryoTEN: Efficiently Enhancing Cryo-EM Density Maps Using Transformers
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2024.09.06.611715
DO 10.1101/2024.09.06.611715
A1 Selvaraj, Joel
A1 Wang, Liguo
A1 Cheng, Jianlin
YR 2024
UL http://biorxiv.org/content/early/2024/09/11/2024.09.06.611715.abstract
AB 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 state- of-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/cryotenCompeting Interest StatementThe authors have declared no competing interest.