Methods for cryo-EM single particle reconstruction of macromolecules having continuous heterogeneity

B Toader, FJ Sigworth, RR Lederman - Journal of molecular biology, 2023 - Elsevier
Macromolecules change their shape (conformation) in the process of carrying out their
functions. The imaging by cryo-electron microscopy of rapidly-frozen, individual copies of …

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 …

HEMNMA-3D: cryo electron tomography method based on normal mode analysis to study continuous conformational variability of macromolecular complexes

M Harastani, M Eltsov, A Leforestier… - Frontiers in molecular …, 2021 - frontiersin.org
Cryogenic electron tomography (cryo-ET) allows structural determination of biomolecules in
their native environment (in situ). Its potential of providing information on the dynamics of …

ContinuousFlex: Software package for analyzing continuous conformational variability of macromolecules in cryo electron microscopy and tomography data

M Harastani, R Vuillemot, I Hamitouche… - Journal of Structural …, 2022 - Elsevier
ContinuousFlex is a user-friendly open-source software package for analyzing continuous
conformational variability of macromolecules in cryo electron microscopy (cryo-EM) and cryo …

Integrating molecular models into CryoEM heterogeneity analysis using scalable high-resolution deep Gaussian mixture models

M Chen, B Toader, R Lederman - Journal of molecular biology, 2023 - Elsevier
Resolving the structural variability of proteins is often key to understanding the structure–
function relationship of those macromolecular machines. Single particle analysis using …

[PDF][PDF] Approximating deformation fields for the analysis of continuous heterogeneity of biological macromolecules by 3D Zernike polynomials

D Herreros, RR Lederman, J Krieger… - IUCrJ, 2021 - journals.iucr.org
Structural biology has evolved greatly due to the advances introduced in fields like electron
microscopy. This image-capturing technique, combined with improved algorithms and …

Survey of the analysis of continuous conformational variability of biological macromolecules by electron microscopy

COS Sorzano, A Jiménez, J Mota, JL Vilas… - … Section F: Structural …, 2019 - journals.iucr.org
Single-particle analysis by electron microscopy is a well established technique for analyzing
the three-dimensional structures of biological macromolecules. Besides its ability to produce …

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 …

Computational biophysics meets cryo‐EM revolution in the search for the functional dynamics of biomolecular systems

MGS Costa, M Gur, JM Krieger… - Wiley Interdisciplinary …, 2024 - Wiley Online Library
There is a variety of experimental and computational techniques available to explore protein
dynamics, each presenting advantages and limitations. One promising experimental …

Hybrid electron microscopy normal mode analysis with scipion

M Harastani, COS Sorzano, S Jonić - Protein Science, 2020 - Wiley Online Library
Abstract Hybrid Electron Microscopy Normal Mode Analysis (HEMNMA) method was
introduced in 2014. HEMNMA computes normal modes of a reference model (an atomic …