Conformational heterogeneity and probability distributions from single-particle cryo-electron microscopy

MDSPACE: Extracting Continuous Conformational Landscapes from Cryo-EM Single Particle Datasets Using 3D-to-2D Flexible Fitting based on Molecular Dynamics Simulation

(2023) Rémi Vuillemot et al.   JOURNAL OF MOLECULAR BIOLOGY

Estimating conformational landscapes from Cryo-EM particles by 3D Zernike polynomials

(2023) D. Herreros et al.   Nature Communications

Energy landscapes from cryo-EM snapshots: a benchmarking study

(2023) Raison Dsouza et al.   Scientific Reports

Effects of cryo-EM cooling on structural ensembles

(2022) Lars V. Bock et al.   BIOPHYSICAL JOURNAL

NMMD: Efficient Cryo-EM Flexible Fitting Based on Simultaneous Normal Mode and Molecular Dynamics atomic displacements

(2022) Rémi Vuillemot et al.   JOURNAL OF MOLECULAR BIOLOGY

Emerging Themes in CryoEM─Single Particle Analysis Image Processing

(2022) Jose Luis Vilas et al.   CHEMICAL REVIEWS

Visualizing Conformational Space of Functional Biomolecular Complexes by Deep Manifold Learning

(2022) Zhaolong Wu et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

DeepHEMNMA: ResNet-based hybrid analysis of continuous conformational heterogeneity in cryo-EM single particle images

(2022) Ilyes Hamitouche et al.   Frontiers in Molecular Biosciences

CryoDRGN: reconstruction of heterogeneous cryo-EM structures using neural networks

(2021) Ellen D. Zhong et al.   NATURE METHODS

Principal component analysis is limited to low-resolution analysis in cryoEM

(2021) Carlos Oscar S. Sorzano et al.   Acta Crystallographica Section D-Structural Biology

A glycan gate controls opening of the SARS-CoV-2 spike protein

(2021) Terra Sztain et al.   Nature Chemistry

Deep learning-based mixed-dimensional Gaussian mixture model for characterizing variability in cryo-EM

(2021) Muyuan Chen et al.   NATURE METHODS

A Bayesian approach to extracting free-energy profiles from cryo-electron microscopy experiments

(2021) Julian Giraldo-Barreto et al.   Scientific Reports

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

(2021) David Herreros et al.   IUCrJ

Energy landscape of domain motion in glutamate dehydrogenase deduced from cryo‐electron microscopy

(2020) Mao Oide et al.   FEBS Journal

Propagation of Conformational Coordinates Across Angular Space in Mapping the Continuum of States from Cryo-EM Data by Manifold Embedding

(2020) Suvrajit Maji et al.   Journal of Chemical Information and Modeling

Simultaneous Determination of Protein Structure and Dynamics Using Cryo-Electron Microscopy

(2018) Massimiliano Bonomi et al.   BIOPHYSICAL JOURNAL

Structure and Conformational Dynamics of the Human Spliceosomal B act Complex

(2018) David Haselbach et al.   CELL

Likelihood-based structural analysis of electron microscopy images

(2018) Pilar Cossio et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Characterisation of molecular motions in cryo-EM single-particle data by multi-body refinement in RELION

(2018) Takanori Nakane et al.   eLife

Biophysical experiments and biomolecular simulations: A perfect match?

(2018) Sandro Bottaro et al.   SCIENCE

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

(2018) C. O. S. Sorzano et al.   Acta Crystallographica Section F-Structural Biology Communications

Continuous changes in structure mapped by manifold embedding of single-particle data in cryo-EM

(2016) Joachim Frank et al.   METHODS

Quantitative Connection between Ensemble Thermodynamics and Single-Molecule Kinetics: A Case Study Using Cryogenic Electron Microscopy and Single-Molecule Fluorescence Resonance Energy Transfer Investigations of the Ribosome

(2015) Colin D. Kinz-Thompson et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Directly reconstructing principal components of heterogeneous particles from cryo-EM images

(2015) Hemant D. Tagare et al.   JOURNAL OF STRUCTURAL BIOLOGY

Covariance Matrix Estimation for the Cryo-EM Heterogeneity Problem

(2015) E. Katsevich et al.   SIAM Journal on Imaging Sciences

Efficient Estimation of Three-Dimensional Covariance and its Application in the Analysis of Heterogeneous Samples in Cryo-Electron Microscopy

(2015) Hstau Y. Liao et al.   STRUCTURE

Trajectories of the ribosome as a Brownian nanomachine

(2014) Ali Dashti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Resolution Revolution

(2014) W. Kuhlbrandt   SCIENCE

Iterative Elastic 3D-to-2D Alignment Method Using Normal Modes for Studying Structural Dynamics of Large Macromolecular Complexes

(2014) Qiyu Jin et al.   STRUCTURE

Bayesian analysis of individual electron microscopy images: Towards structures of dynamic and heterogeneous biomolecular assemblies

(2013) Pilar Cossio et al.   JOURNAL OF STRUCTURAL BIOLOGY

How Fast-Folding Proteins Fold

(2011) K. Lindorff-Larsen et al.   SCIENCE

Identifying Conformational States of Macromolecules by Eigen-Analysis of Resampled Cryo-EM Images

(2011) Pawel A. Penczek et al.   STRUCTURE

Ribosome dynamics and tRNA movement by time-resolved electron cryomicroscopy

(2010) Niels Fischer et al.   NATURE