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

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

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

Multi-Scale Flexible Fitting of Proteins to Cryo-EM Density Maps at Medium Resolution

(2021) Marta Kulik et al.   Frontiers in Molecular Biosciences

HEMNMA-3D: Cryo Electron Tomography Method Based on Normal Mode Analysis to Study Continuous Conformational Variability of Macromolecular Complexes

(2021) Mohamad Harastani et al.   Frontiers in Molecular Biosciences

High-resolution cryo-EM structure of photosystem II reveals damage from high-dose electron beams

(2021) Koji Kato et al.   Communications Biology

Efficient Flexible Fitting Refinement with Automatic Error Fixing for De Novo Structure Modeling from Cryo-EM Density Maps

(2021) Takaharu Mori et al.   Journal of Chemical Information and Modeling

3D variability analysis: Resolving continuous flexibility and discrete heterogeneity from single particle cryo-EM

(2021) Ali Punjani et al.   JOURNAL OF STRUCTURAL BIOLOGY

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

(2021) Muyuan Chen et al.   NATURE METHODS

TomoFlow: Analysis of Continuous Conformational Variability of Macromolecules in Cryogenic Subtomograms based on 3D Dense Optical Flow

(2021) Mohamad Harastani et al.   JOURNAL OF MOLECULAR BIOLOGY

Advances in Xmipp for Cryo–Electron Microscopy: From Xmipp to Scipion

(2021) David Strelak et al.   MOLECULES

Single-particle cryo-EM at atomic resolution

(2020) Takanori Nakane et al.   NATURE

In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges

(2020) Beata Turoňová et al.   SCIENCE

Retrieving functional pathways of biomolecules from single-particle snapshots

(2020) Ali Dashti et al.   Nature Communications

Conformation space of a heterodimeric ABC exporter under turnover conditions

(2019) Susanne Hofmann et al.   NATURE

Hybrid Electron Microscopy Normal Mode Analysis with Scipion

(2019) Mohamad Harastani et al.   PROTEIN SCIENCE

In Situ Structure of an Intact Lipopolysaccharide-Bound Bacterial Surface Layer

(2019) Andriko von Kügelgen et al.   CELL

emClarity: software for high-resolution cryo-electron tomography and subtomogram averaging

(2018) Benjamin A. Himes et al.   NATURE METHODS

Acceleration of cryo-EM Flexible Fitting for Large Biomolecular Systems by Efficient Space Partitioning

(2018) Takaharu Mori et al.   STRUCTURE

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

GENESIS 1.1: A hybrid-parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms

(2017) Chigusa Kobayashi et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Flexible fitting to cryo-EM density map using ensemble molecular dynamics simulations

(2017) Osamu Miyashita et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Three-dimensional CTF correction improves the resolution of electron tomograms

(2017) Michael Kunz et al.   JOURNAL OF STRUCTURAL BIOLOGY

Structure and assembly of the Ebola virus nucleocapsid

(2017) William Wan et al.   NATURE

UCSF ChimeraX: Meeting modern challenges in visualization and analysis

(2017) Thomas D. Goddard et al.   PROTEIN SCIENCE

StructMap: Elastic Distance Analysis of Electron Microscopy Maps for Studying Conformational Changes

(2016) Carlos Oscar Sanchez Sorzano et al.   BIOPHYSICAL JOURNAL

Coarse-Graining of Volumes for Modeling of Structure and Dynamics in Electron Microscopy: Algorithm to Automatically Control Accuracy of Approximation

(2016) Slavica Jonic et al.   IEEE Journal of Selected Topics in Signal Processing

Scipion: A software framework toward integration, reproducibility and validation in 3D electron microscopy

(2016) J.M. de la Rosa-Trevín et al.   JOURNAL OF STRUCTURAL BIOLOGY

An atomic model of HIV-1 capsid-SP1 reveals structures regulating assembly and maturation

(2016) Florian K. M. Schur et al.   SCIENCE

2.3 A resolution cryo-EM structure of human p97 and mechanism of allosteric inhibition

(2016) S. Banerjee et al.   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

CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data

(2013) Jing Huang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Fast and accurate reference-free alignment of subtomograms

(2013) Yuxiang Chen et al.   JOURNAL OF STRUCTURAL BIOLOGY

Structure of the TRPV1 ion channel determined by electron cryo-microscopy

(2013) Maofu Liao et al.   NATURE

Nonlocal Transform-Domain Filter for Volumetric Data Denoising and Reconstruction

(2012) M. Maggioni et al.   IEEE TRANSACTIONS ON IMAGE PROCESSING

Flexible Fitting of High-Resolution X-Ray Structures into Cryoelectron Microscopy Maps Using Biased Molecular Dynamics Simulations

(2008) Marek Orzechowski et al.   BIOPHYSICAL JOURNAL

Flexible Fitting of Atomic Structures into Electron Microscopy Maps Using Molecular Dynamics

(2008) Leonardo G. Trabuco et al.   STRUCTURE

Classification of cryo-electron sub-tomograms using constrained correlation

(2007) Friedrich Förster et al.   JOURNAL OF STRUCTURAL BIOLOGY