3DFlex: determining structure and motion of flexible proteins from cryo-EM

Neural Fields in Visual Computing and Beyond

(2022) Yiheng Xie et al.   COMPUTER GRAPHICS FORUM

Neural representations of cryo-EM maps and a graph-based interpretation

(2022) Nathan Ranno et al.   BMC BIOINFORMATICS

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

Cryo-EM Reveals Integrin-Mediated TGF-β Activation without Release from Latent TGF-β

(2020) Melody G. Campbell et al.   CELL

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

Retrieving functional pathways of biomolecules from single-particle snapshots

(2020) Ali Dashti et al.   Nature Communications

Continuous flexibility analysis of SARS-CoV-2 spike prefusion structures

(2020) Roberto Melero et al.   IUCrJ

Non-uniform refinement: adaptive regularization improves single-particle cryo-EM reconstruction

(2020) Ali Punjani et al.   NATURE METHODS

Challenges and opportunities in cryo-EM single-particle analysis

(2019) Dmitry Lyumkis   JOURNAL OF BIOLOGICAL CHEMISTRY

Cryo-EM reconstruction of continuous heterogeneity by Laplacian spectral volumes

(2019) Amit Moscovich et al.   INVERSE PROBLEMS

Hyper-molecules: on the representation and recovery of dynamical structures for applications in flexible macro-molecules in cryo-EM

(2019) Roy R Lederman et al.   INVERSE PROBLEMS

Structural Variability from Noisy Tomographic Projections

(2018) Joakim Andén et al.   SIAM Journal on Imaging Sciences

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

(2018) Takanori Nakane et al.   eLife

cisTEM, user-friendly software for single-particle image processing

(2018) Timothy Grant et al.   eLife

Structures of transcription pre-initiation complex with TFIIH and Mediator

(2017) S. Schilbach et al.   NATURE

cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination

(2017) Ali Punjani et al.   NATURE METHODS

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

(2016) Joachim Frank et al.   METHODS

TRPV1 structures in nanodiscs reveal mechanisms of ligand and lipid action

(2016) Yuan Gao et al.   NATURE

Cryo-EM structure of the yeast U4/U6.U5 tri-snRNP at 3.7 Å resolution

(2016) Thi Hoang Duong Nguyen et al.   NATURE

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

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

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

RELION: Implementation of a Bayesian approach to cryo-EM structure determination

(2012) Sjors H.W. Scheres   JOURNAL OF STRUCTURAL BIOLOGY

Prevention of overfitting in cryo-EM structure determination

(2012) Sjors H W Scheres et al.   NATURE METHODS

A Bayesian View on Cryo-EM Structure Determination

(2011) Sjors H.W. Scheres   JOURNAL OF MOLECULAR BIOLOGY

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

(2011) Pawel A. Penczek et al.   STRUCTURE

Quantitative analysis of cryo-EM density map segmentation by watershed and scale-space filtering, and fitting of structures by alignment to regions

(2010) Grigore D. Pintilie et al.   JOURNAL OF STRUCTURAL BIOLOGY