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 …

A robust single-particle cryo-electron microscopy (cryo-EM) processing workflow with cryoSPARC, RELION, and Scipion

MC DiIorio, AW Kulczyk - JoVE (Journal of Visualized Experiments), 2022 - jove.com
Recent advances in both instrumentation and image processing software have made single-
particle cryo-electron microscopy (cryo-EM) the preferred method for structural biologists to …

Scipion-EM-ProDy: A Graphical Interface for the ProDy Python Package within the Scipion Workflow Engine Enabling Integration of Databases, Simulations and Cryo …

JM Krieger, COS Sorzano, JM Carazo - International Journal of Molecular …, 2023 - mdpi.com
Macromolecular assemblies, such as protein complexes, undergo continuous structural
dynamics, including global reconfigurations critical for their function. Two fast analytical …

Use of Localized Reconstruction to Visualize the Shigella Phage Sf6 Tail Apparatus

CFD Hou, F Li, S Iglesias, G Cingolani - Bacteriophages: Methods and …, 2023 - Springer
Cryogenic electron microscopy (cryo-EM) single-particle analysis has revolutionized the
structural analysis of icosahedral viruses, including tailed bacteriophages. In recent years …

A fast image alignment approach for 2D classification of cryo-EM images using spectral clustering

X Wang, Y Lu, J Liu - Current Issues in Molecular Biology, 2021 - mdpi.com
Three-dimensional (3D) reconstruction in single-particle cryo-electron microscopy (cryo-EM)
is a significant technique for recovering the 3D structure of proteins or other biological …

Umpalumpa: a framework for efficient execution of complex image processing workloads on heterogeneous nodes

D Střelák, D Myška, F Petrovič, J Polák, J Ol'ha… - Computing, 2023 - Springer
Modern computers are typically heterogeneous devices—besides the standard central
processing unit (CPU), they commonly include an accelerator such as a graphics processing …

[HTML][HTML] A new algorithm for particle weighted subtraction to decrease signals from unwanted components in single particle analysis

E Fernandez-Gimenez, MM Martínez… - Journal of Structural …, 2023 - Elsevier
Single particle analysis (SPA) in cryo-electron microscopy (cryo-EM) is highly used to obtain
the near-atomic structure of biological macromolecules. The current methods allow users to …

[HTML][HTML] The Structure of Spiroplasma Virus 4: Exploring the Capsid Diversity of the Microviridae

M Mietzsch, S Kailasan, A Bennett, P Chipman, B Fane… - Viruses, 2024 - mdpi.com
Spiroplasma virus 4 (SpV4) is a bacteriophage of the Microviridae, which packages circular
ssDNA within non-enveloped T= 1 icosahedral capsids. It infects spiroplasmas, which are …

[HTML][HTML] Local defocus estimation in single particle analysis in cryo-electron microscopy

E Fernandez-Gimenez, JM Carazo… - Journal of Structural …, 2023 - Elsevier
Single Particle analysis (SPA) aims to determine the three-dimensional structure of proteins
and macromolecular complexes. The current state of the art has allowed us to achieve near …

Heterogeneous cryo-EM projection image classification using a two-stage spectral clustering based on novel distance measures

X Wang, Y Lu, X Lin - Briefings in Bioinformatics, 2022 - academic.oup.com
Single-particle cryo-electron microscopy (cryo-EM) has become one of the mainstream
technologies in the field of structural biology to determine the three-dimensional (3D) …