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Constructing of molecular structural models from Cryo-Electron Microscopy (Cryo-EM) density volumes is the critical last step of structure determination by Cryo-EM technologies. Methods have evolved from manual construction by structural…

Machine Learning · Computer Science 2019-02-13 Kui Xu , Zhe Wang , Jiangping Shi , Hongsheng Li , Qiangfeng Cliff Zhang

Cryo-electron microscopy (cryo-EM) allows for the high-resolution reconstruction of 3D structures of proteins and other biomolecules. Successful reconstruction of both shape and movement greatly helps understand the fundamental processes of…

Computer Vision and Pattern Recognition · Computer Science 2023-10-12 Xinhang Liu , Yan Zeng , Yifan Qin , Hao Li , Jiakai Zhang , Lan Xu , Jingyi Yu

Cryo-electron microscopy (cryo-EM) has become a major experimental technique to determine the structures of large protein complexes and molecular assemblies, as evidenced by the 2017 Nobel Prize. Although cryo-EM has been drastically…

Biomolecules · Quantitative Biology 2021-06-01 Dong Si , Andrew Nakamura , Runbang Tang , Haowen Guan , Jie Hou , Ammaar Firozi , Renzhi Cao , Kyle Hippe , Minglei Zhao

Single-particle cryo-electron microscopy (cryo-EM) has recently joined X-ray crystallography and NMR spectroscopy as a high-resolution structural method to resolve biological macromolecules. In a cryo-EM experiment, the microscope produces…

Information Theory · Computer Science 2022-10-28 Tamir Bendory , Nicolas Boumal , William Leeb , Eitan Levin , Amit Singer

Cryo-electron microscopy (cryo-EM) is a powerful imaging technique for reconstructing three-dimensional molecular structures from noisy tomographic projection images of randomly oriented particles. We introduce a new data fusion framework,…

Computer Vision and Pattern Recognition · Computer Science 2025-12-15 Joe Kileel , Oscar Mickelin , Amit Singer , Sheng Xu

The three-dimensional structure of proteins plays a crucial role in determining their function. Protein structure prediction methods, like AlphaFold, offer rapid access to a protein structure. However, large protein complexes cannot be…

Biomolecules · Quantitative Biology 2025-03-05 Gabriel Ducrocq , Lukas Grunewald , Sebastian Westenhoff , Fredrik Lindsten

Single-particle electron cryomicroscopy is an essential tool for high-resolution 3D reconstruction of proteins and other biological macromolecules. An important challenge in cryo-EM is the reconstruction of non-rigid molecules with parts…

Image and Video Processing · Electrical Eng. & Systems 2021-05-31 Amit Moscovich , Amit Halevi , Joakim Andén , Amit Singer

Single particle cryo-electron microscopy has become a critical tool in structural biology over the last decade, able to achieve atomic scale resolution in three dimensional models from hundreds of thousands of (noisy) two-dimensional…

Numerical Analysis · Mathematics 2023-07-19 Aaditya V. Rangan , Leslie Greengard

Protein structure prediction models are now capable of generating accurate 3D structural hypotheses from sequence alone. However, they routinely fail to capture the conformational diversity of dynamic biomolecular complexes, often requiring…

Machine Learning · Computer Science 2025-12-02 Rishwanth Raghu , Axel Levy , Gordon Wetzstein , Ellen D. Zhong

Cryo-electron tomography (cryo-ET) is an imaging technique that allows three-dimensional visualization of macro-molecular assemblies under near-native conditions. Cryo-ET comes with a number of challenges, mainly low signal-to-noise and…

Enhancing cryogenic electron microscopy (cryo-EM) 3D density maps at intermediate resolution (4-8 {\AA}) is crucial in protein structure determination. Recent advances in deep learning have led to the development of automated approaches for…

Computer Vision and Pattern Recognition · Computer Science 2025-05-16 Chenwei Zhang , Khanh Dao Duc

Cryo-electron microscopy (cryo-EM) emerges as a pivotal technology for determining the architecture of cells, viruses, and protein assemblies at near-atomic resolution. Traditional particle picking, a key step in cryo-EM, struggles with…

Biomolecules · Quantitative Biology 2024-04-17 Chentianye Xu , Xueying Zhan , Min Xu

Cryo-electron microscopy (cryo-EM) is an experimental technique for protein structure determination that images an ensemble of macromolecules in near-physiological contexts. While recent advances enable the reconstruction of dynamic…

Cryo-EM is an increasingly popular method for determining the atomic resolution 3D structure of macromolecular complexes (eg, proteins) from noisy 2D images captured by an electron microscope. The computational task is to reconstruct the 3D…

Computer Vision and Pattern Recognition · Computer Science 2024-10-04 Shayan Shekarforoush , David B. Lindell , Marcus A. Brubaker , David J. Fleet

Single-particle cryo-electron microscopy (cryo-EM) is an emerging imaging modality capable of visualizing proteins and macro-molecular complexes at near-atomic resolution. The low electron-doses used to prevent sample radiation damage,…

Image and Video Processing · Electrical Eng. & Systems 2020-11-24 Qinwen Huang , Ye Zhou , Xiaochen Du , Reed Chen , Jianyou Wang , Cynthia Rudin , Alberto Bartesaghi

Cryo-electron microscopy (cryo-EM) is an indispensable technique for determining the 3D structures of dynamic biomolecular complexes. While typically applied to image a single molecular species, cryo-EM has the potential for structure…

Computer Vision and Pattern Recognition · Computer Science 2026-03-23 Jeffrey Gu , Minkyu Jeon , Ambri Ma , Serena Yeung-Levy , Ellen D. Zhong

Cryo-electron microscopy (Cryo-EM) enables high-resolution imaging of biomolecules, but structural heterogeneity remains a major challenge in 3D reconstruction. Traditional methods assume a discrete set of conformations, limiting their…

Machine Learning · Statistics 2025-09-09 Diego Sanchez Espinosa , Erik H Thiede , Yunan Yang

In the past decade, deep conditional generative models have revolutionized the generation of realistic images, extending their application from entertainment to scientific domains. Single-particle cryo-electron microscopy (cryo-EM) is…

Computer Vision and Pattern Recognition · Computer Science 2024-10-01 Jiakai Zhang , Qihe Chen , Yan Zeng , Wenyuan Gao , Xuming He , Zhijie Liu , Jingyi Yu

Cryo-electron microscopy (cryo-EM) has revolutionized experimental protein structure determination. Despite advances in high resolution reconstruction, a majority of cryo-EM experiments provide either a single state of the studied…

Single particle electron cryomicroscopy (cryo-EM) allows for structures of proteins and protein complexes to be determined from images of non-crystalline specimens. Cryo-EM data analysis requires electron microscope images of randomly…

Instrumentation and Detectors · Physics 2015-11-23 Jianhua Zhao , Marcus A. Brubaker , Samir Benlekbir , John L. Rubinstein