Related references
Note: Only part of the references are listed.CryoDRGN: reconstruction of heterogeneous cryo-EM structures using neural networks
Ellen D. Zhong et al.
NATURE METHODS (2021)
Deep learning-based mixed-dimensional Gaussian mixture model for characterizing variability in cryo-EM
Muyuan Chen et al.
NATURE METHODS (2021)
Energy landscape of domain motion in glutamate dehydrogenase deduced from cryo-electron microscopy
Mao Oide et al.
FEBS JOURNAL (2020)
Hyper-molecules: on the representation and recovery of dynamical structures for applications in flexible macro-molecules in cryo-EM
Roy R. Lederman et al.
INVERSE PROBLEMS (2020)
POLARIS: Path of Least Action Analysis on Energy Landscapes
Evan Seitz et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2020)
Heightened Cold-Denaturation of Proteins at the Ice-Water Interface
Andrea Arsiccio et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2020)
Single-particle cryo-EM at atomic resolution
Takanori Nakane et al.
NATURE (2020)
Retrieving functional pathways of biomolecules from single-particle snapshots
Ali Dashti et al.
NATURE COMMUNICATIONS (2020)
Data-guided Multi-Map variables for ensemble refinement of molecular movies
John W. Vant et al.
JOURNAL OF CHEMICAL PHYSICS (2020)
Cryo-EM Studies of TMEM16F Calcium-Activated Ion Channel Suggest Features Important for Lipid Scrambling
Shengjie Feng et al.
CELL REPORTS (2019)
Neural-Network-Based Path Collective Variables for Enhanced Sampling of Phase Transformations
Jutta Rogal et al.
PHYSICAL REVIEW LETTERS (2019)
STABILITY AND CONVERGENCE OF THE STRING METHOD FOR COMPUTING MINIMUM ENERGY PATHS
Brian Van Koten et al.
MULTISCALE MODELING & SIMULATION (2019)
Cryo-electron microscopy for structural analysis of dynamic biological macromolecules
Kazuyoshi Murata et al.
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS (2018)
Simultaneous Determination of Protein Structure and Dynamics Using Cryo-Electron Microscopy
Massimiliano Bonomi et al.
BIOPHYSICAL JOURNAL (2018)
Structure and Conformational Dynamics of the Human Spliceosomal Bact Complex
David Haselbach et al.
CELL (2018)
Likelihood-based structural analysis of electron microscopy images
Pilar Cossio et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2018)
SWISS-MODEL: homology modelling of protein structures and complexes
Andrew Waterhouse et al.
NUCLEIC ACIDS RESEARCH (2018)
Structural Variability from Noisy Tomographic Projections
Joakim Anden et al.
SIAM JOURNAL ON IMAGING SCIENCES (2018)
Bayesian inference of rotor ring stoichiometry from electron microscopy images of archaeal ATP synthase
Pilar Cossio et al.
MICROSCOPY (2018)
Girsanov reweighting for metadynamics simulations
Luca Donati et al.
JOURNAL OF CHEMICAL PHYSICS (2018)
Automated design of collective variables using supervised machine learning
Mohammad M. Sultan et al.
JOURNAL OF CHEMICAL PHYSICS (2018)
CHARMM36m: an improved force field for folded and intrinsically disordered proteins
Jing Huang et al.
NATURE METHODS (2017)
cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination
Ali Punjani et al.
NATURE METHODS (2017)
The HSP90 chaperone machinery
Florian H. Schopf et al.
NATURE REVIEWS MOLECULAR CELL BIOLOGY (2017)
Computational methods for analyzing conformational variability of macromolecular complexes from cryo-electron microscopy images
Slavica Jonic
CURRENT OPINION IN STRUCTURAL BIOLOGY (2017)
BioEM: GPU-accelerated computing of Bayesian inference of electron microscopy images
Pilar Cossio et al.
COMPUTER PHYSICS COMMUNICATIONS (2017)
Continuous changes in structure mapped by manifold embedding of single-particle data in cryo-EM
Joachim Frank et al.
METHODS (2016)
EMPIAR: a public archive for raw electron microscopy image data
Andrii Iudin et al.
NATURE METHODS (2016)
A Primer to Single-Particle Cryo-Electron Microscopy
Yifan Cheng et al.
CELL (2015)
Directly reconstructing principal components of heterogeneous particles from cryo-EM images
Hemant D. Tagare et al.
JOURNAL OF STRUCTURAL BIOLOGY (2015)
Covariance Matrix Estimation for the Cryo-EM Heterogeneity Problem
E. Katsevich et al.
SIAM JOURNAL ON IMAGING SCIENCES (2015)
Efficient Estimation of Three-Dimensional Covariance and its Application in the Analysis of Heterogeneous Samples in Cryo-Electron Microscopy
Hstau Y. Liao et al.
STRUCTURE (2015)
Do's and Don'ts of Cryo-electron Microscopy: A Primer on Sample Preparation and High Quality Data Collection for Macromolecular 3D Reconstruction
Vanessa Cabra et al.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS (2015)
PLUMED 2: New feathers for an old bird
Gareth A. Tribello et al.
COMPUTER PHYSICS COMMUNICATIONS (2014)
Free Energy Surface Reconstruction from Umbrella Samples Using Gaussian Process Regression
Thomas Stecher et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2014)
Trajectories of the ribosome as a Brownian nanomachine
Ali Dashti et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)
Iterative Elastic 3D-to-2D Alignment Method Using Normal Modes for Studying Structural Dynamics of Large Macromolecular Complexes
Qiyu Jin et al.
STRUCTURE (2014)
Bayesian analysis of individual electron microscopy images: Towards structures of dynamic and heterogeneous biomolecular assemblies
Pilar Cossio et al.
JOURNAL OF STRUCTURAL BIOLOGY (2013)
Requirement of Ca2+ Ions for the Hyperthermostability of Tk-Subtilisin from Thermococcus kodakarensis
Ryo Uehara et al.
BIOCHEMISTRY (2012)
RELION: Implementation of a Bayesian approach to cryo-EM structure determination
Sjors H. W. Scheres
JOURNAL OF STRUCTURAL BIOLOGY (2012)
Structural characterization of mRNA-tRNA translocation intermediates
Xabier Agirrezabala et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)
Splitting Probabilities as a Test of Reaction Coordinate Choice in Single-Molecule Experiments
John D. Chodera et al.
PHYSICAL REVIEW LETTERS (2011)
Identifying Conformational States of Macromolecules by Eigen-Analysis of Resampled Cryo-EM Images
Pawel A. Penczek et al.
STRUCTURE (2011)
Generating Uniform Incremental Grids on SO(3) Using the Hopf Fibration
Anna Yershova et al.
INTERNATIONAL JOURNAL OF ROBOTICS RESEARCH (2010)
Ribosome dynamics and tRNA movement by time-resolved electron cryomicroscopy
Niels Fischer et al.
NATURE (2010)
Improved side-chain torsion potentials for the Amber ff99SB protein force field
Kresten Lindorff-Larsen et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2010)
Software news and updates - CHARNIM-GUI: A web-based grraphical user interface for CHARMM
Sunhwan Jo et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2008)
Finding transition pathways using the string method with swarms of trajectories
Albert C. Pan et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2008)
Image processing for electron microscopy single-particle analysis using XMIPP
Sjors H. W. Scheres et al.
NATURE PROTOCOLS (2008)
From A to B in free energy space
Davide Branduardi et al.
JOURNAL OF CHEMICAL PHYSICS (2007)
Canonical sampling through velocity rescaling
Giovanni Bussi et al.
JOURNAL OF CHEMICAL PHYSICS (2007)
String method in collective variables: Minimum free energy paths and isocommittor surfaces
Luca Maragliano et al.
JOURNAL OF CHEMICAL PHYSICS (2006)
Crystal structure of an Hsp90-nucleotide-p23/Sba1 closed chaperone complex
MMU Ali et al.
NATURE (2006)
From transition paths to transition states and rate coefficients
G Hummer
JOURNAL OF CHEMICAL PHYSICS (2004)
Escaping free-energy minima
A Laio et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)