Single-particle cryo-electron microscopy: Mathematical theory, computational challenges, and opportunities

T Bendory, A Bartesaghi… - IEEE signal processing …, 2020 - ieeexplore.ieee.org
In recent years, an abundance of new molecular structures have been elucidated using cryo-
electron microscopy (cryo-EM), largely due to advances in hardware technology and data …

Deep learning in electron microscopy

JM Ede - Machine Learning: Science and Technology, 2021 - iopscience.iop.org
Deep learning is transforming most areas of science and technology, including electron
microscopy. This review paper offers a practical perspective aimed at developers with …

DeepEMhancer: a deep learning solution for cryo-EM volume post-processing

R Sanchez-Garcia, J Gomez-Blanco, A Cuervo… - Communications …, 2021 - nature.com
Cryo-EM maps are valuable sources of information for protein structure modeling. However,
due to the loss of contrast at high frequencies, they generally need to be post-processed to …

Applications of deep learning in electron microscopy

KP Treder, C Huang, JS Kim, AI Kirkland - Microscopy, 2022 - academic.oup.com
We review the growing use of machine learning in electron microscopy (EM) driven in part
by the availability of fast detectors operating at kiloHertz frame rates leading to large data …

Extraction of protein dynamics information from cryo-EM maps using deep learning

S Matsumoto, S Ishida, M Araki, T Kato… - Nature Machine …, 2021 - nature.com
Elucidation of both the three-dimensional structure and the dynamics of a protein is essential
to understand its function. Technical breakthroughs in single-particle analysis based on cryo …

[HTML][HTML] Structures of the promoter-bound respiratory syncytial virus polymerase

D Cao, Y Gao, Z Chen, I Gooneratne, C Roesler… - Nature, 2024 - nature.com
The respiratory syncytial virus (RSV) polymerase is a multifunctional RNA-dependent RNA
polymerase composed of the large (L) protein and the phosphoprotein (P). It transcribes the …

Deep learning to predict protein backbone structure from high-resolution cryo-EM density maps

D Si, SA Moritz, J Pfab, J Hou, R Cao, L Wang, T Wu… - Scientific reports, 2020 - nature.com
Cryo-electron microscopy (cryo-EM) has become a leading technology for determining
protein structures. Recent advances in this field have allowed for atomic resolution …

Emerging themes in CryoEM─ Single particle analysis image processing

JL Vilas, JM Carazo, COS Sorzano - Chemical Reviews, 2022 - ACS Publications
Cryo-electron microscopy (CryoEM) has become a vital technique in structural biology. It is
an interdisciplinary field that takes advantage of advances in biochemistry, physics, and …

[HTML][HTML] DeepRes: a new deep-learning-and aspect-based local resolution method for electron-microscopy maps

E Ramírez-Aportela, J Mota, P Conesa, JM Carazo… - IUCrJ, 2019 - journals.iucr.org
In this article, a method is presented to estimate a new local quality measure for 3D cryoEM
maps that adopts the form of alocal resolution'type of information. The algorithm (DeepRes) …

Cryo-EM structure of the respiratory syncytial virus RNA polymerase

D Cao, Y Gao, C Roesler, S Rice, P D'Cunha… - Nature …, 2020 - nature.com
The respiratory syncytial virus (RSV) RNA polymerase, constituted of a 250 kDa large (L)
protein and tetrameric phosphoprotein (P), catalyzes three distinct enzymatic activities …