biostudies-literatureSelvaraj JNational Institutes of HealthNIH HHSNIGMS NIH HHSbtaf092https://www.ebi.ac.uk/biostudies/studies/S-EPMC11906401biostudies-literatureUnknown41(3)<h4>Motivation</h4>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.<h4>Results</h4>In this study, we introduce CryoTEN-a 3D UNETR++ style transformer to improve cryo-EM maps effectively. CryoTEN is trained using a diverse set of 1295 cryo-EM maps as inputs and their correspoBioinformatics (Oxford, England)CryoTEN: efficiently enhancing cryo-EM density maps using transformers.PMC11906401R01GM146340R01 GM146340Selvaraj JWang LCheng JfalseCryoTEN: efficiently enhancing cryo-EM density maps using transformers.<h4>Motivation</h4>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.<h4>Results</h4>In this study, we introduce CryoTEN-a 3D UNETR++ style transformer to improve cryo-EM maps effectively. CryoTEN is trained using a diverse set of 1295 cryo-EM maps as inputs and their correspo2025-01-01T00:00:00Z2025 Mar2026-06-01T10:11:30.962Z2025-04-04T14:47:15.323ZS-EPMC119064014003658810.1093/bioinformatics/btaf092