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 …

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 …

MonoRes: automatic and accurate estimation of local resolution for electron microscopy maps

JL Vilas, J Gómez-Blanco, P Conesa, R Melero… - Structure, 2018 - cell.com
Since the beginning of electron microscopy, resolution has been a critical parameter. In this
article, we propose a fully automatic, accurate method for determining the local resolution of …

[PDF][PDF] On bias, variance, overfitting, gold standard and consensus in single-particle analysis by cryo-electron microscopy

COS Sorzano, A Jiménez-Moreno… - … Section D: Structural …, 2022 - journals.iucr.org
Cryo-electron microscopy (cryoEM) has become a well established technique to elucidate
the 3D structures of biological macromolecules. Projection images from thousands of …

New measures of anisotropy of cryo-EM maps

JL Vilas, HD Tagare - Nature Methods, 2023 - nature.com
We propose two new measures of resolution anisotropy for cryogenic electron microscopy
maps: Fourier shell occupancy (FSO), and the Bingham test (BT). FSO varies from 1 to 0 …

[PDF][PDF] 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) …

The resolution in X-ray crystallography and single-particle cryogenic electron microscopy

VRA Dubach, A Guskov - Crystals, 2020 - mdpi.com
X-ray crystallography and single-particle analysis cryogenic electron microscopy are
essential techniques for uncovering the three-dimensional structures of biological …

FSC-Q: a CryoEM map-to-atomic model quality validation based on the local Fourier shell correlation

E Ramírez-Aportela, D Maluenda, YC Fonseca… - Nature …, 2021 - nature.com
In recent years, advances in cryoEM have dramatically increased the resolution of
reconstructions and, with it, the number of solved atomic models. It is widely accepted that …

Advances in xmipp for cryo–electron microscopy: From xmipp to scipion

D Strelak, A Jiménez-Moreno, JL Vilas… - Molecules, 2021 - mdpi.com
Xmipp is an open-source software package consisting of multiple programs for processing
data originating from electron microscopy and electron tomography, designed and managed …

Non-uniformity of projection distributions attenuates resolution in Cryo-EM

PR Baldwin, D Lyumkis - Progress in biophysics and molecular biology, 2020 - Elsevier
Virtually all single-particle cryo-EM experiments currently suffer from specimen adherence to
the air-water interface, leading to a non-uniform distribution in the set of projection views …