Integrating Molecular Models Into CryoEM Heterogeneity Analysis Using Scalable High-resolution Deep Gaussian Mixture Models

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

Beyond the Backbone: The Next Generation of Pathwalking Utilities for Model Building in CryoEM Density Maps

(2022) Corey F. Hryc et al.   Biomolecules

Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1

(2022) Michael Prattes et al.   NATURE STRUCTURAL & 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

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

(2021) Erney Ramírez-Aportela et al.   Nature Communications

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

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

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

Validation, analysis and annotation of cryo-EM structures

(2021) Grigore Pintilie et al.   Acta Crystallographica Section D-Structural Biology

Mapping the catalytic conformations of an assembly-line polyketide synthase module

(2021) Dillon P. Cogan et al.   SCIENCE

Activation of the GLP-1 receptor by a non-peptidic agonist

(2020) Peishen Zhao et al.   NATURE

Measurement of atom resolvability in cryo-EM maps with Q-scores

(2020) Grigore Pintilie et al.   NATURE METHODS

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

Deep Learning to Predict Protein Backbone Structure from High-Resolution Cryo-EM Density Maps

(2020) Dong Si et al.   Scientific Reports

Cryo-EM structures and dynamics of substrate-engaged human 26S proteasome

(2018) Yuanchen Dong et al.   NATURE

Structure of a pre-catalytic spliceosome

(2017) Clemens Plaschka et al.   NATURE

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

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

Structural Basis for Gating and Activation of RyR1

(2016) Amédée des Georges et al.   CELL

De Novo modeling in cryo-EM density maps with Pathwalking

(2016) Muyuan Chen et al.   JOURNAL OF STRUCTURAL BIOLOGY

High resolution single particle refinement in EMAN2.1

(2016) James M. Bell et al.   METHODS

TRPV1 structures in nanodiscs reveal mechanisms of ligand and lipid action

(2016) Yuan Gao et al.   NATURE

Gating machinery of InsP3R channels revealed by electron cryomicroscopy

(2015) Guizhen Fan et al.   NATURE