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

Structure and Conformational Dynamics of the Human Spliceosomal B act Complex

(2018) David Haselbach et al.   CELL

Multiscale virtual particle based elastic network model (MVP-ENM) for normal mode analysis of large-sized biomolecules

(2018) Kelin Xia   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Structural Variability from Noisy Tomographic Projections

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

Fluctuating Finite Element Analysis (FFEA): A continuum mechanics software tool for mesoscale simulation of biomolecules

(2018) Albert Solernou et al.   PLoS Computational Biology

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

Langevin Dynamics with Variable Coefficients and Nonconservative Forces: From Stationary States to Numerical Methods

(2017) Matthias Sachs et al.   Entropy

NOLB: Nonlinear Rigid Block Normal-Mode Analysis Method

(2017) Alexandre Hoffmann et al.   Journal of Chemical Theory and Computation

Jumping between protein conformers using normal modes

(2017) Swapnil Mahajan et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Relation between Protein Intrinsic Normal Mode Weights and Pre-Existing Conformer Populations

(2017) Beytullah Ozgur et al.   JOURNAL OF PHYSICAL CHEMISTRY B

cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination

(2017) Ali Punjani et al.   NATURE METHODS

Data-driven coarse graining of large biomolecular structures

(2017) Yi-Ling Chen et al.   PLoS One

A probabilistic model for detecting rigid domains in protein structures

(2016) Thach Nguyen et al.   BIOINFORMATICS

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

New generation of elastic network models

(2016) José Ramón López-Blanco et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

Effect of Clustering Algorithm on Establishing Markov State Model for Molecular Dynamics Simulations

(2016) Yan Li et al.   Journal of Chemical Information and Modeling

ClustENM: ENM-Based Sampling of Essential Conformational Space at Full Atomic Resolution

(2016) Zeynep Kurkcuoglu et al.   Journal of Chemical Theory and Computation

Robust Density-Based Clustering To Identify Metastable Conformational States of Proteins

(2016) Florian Sittel et al.   Journal of Chemical Theory and Computation

Local analysis of strains and rotations for macromolecular electron microscopy maps

(2016) C.O.S. Sorzano et al.   JOURNAL OF STRUCTURAL BIOLOGY

Denoising of high-resolution single-particle electron-microscopy density maps by their approximation using three-dimensional Gaussian functions

(2016) S. Jonić et al.   JOURNAL OF STRUCTURAL BIOLOGY

Methods to account for movement and flexibility in cryo-EM data processing

(2016) S. Rawson et al.   METHODS

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

(2016) Joachim Frank et al.   METHODS

Versatility of Approximating Single-Particle Electron Microscopy Density Maps Using Pseudoatoms and Approximation-Accuracy Control

(2016) Slavica Jonić et al.   Biomed Research International

Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2

(2016) Dari Kimanius et al.   eLife

Modeling Structural Dynamics of Biomolecular Complexes by Coarse-Grained Molecular Simulations

(2015) Shoji Takada et al.   ACCOUNTS OF CHEMICAL RESEARCH

Modelling biomacromolecular assemblies with continuum mechanics

(2015) Benjamin Hanson et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

cNMA: a framework of encounter complex-based normal mode analysis to model conformational changes in protein interactions

(2015) Tomasz Oliwa et al.   BIOINFORMATICS

Structure-Encoded Global Motions and Their Role in Mediating Protein-Substrate Interactions

(2015) Ivet Bahar et al.   BIOPHYSICAL JOURNAL

Internal Normal Mode Analysis (iNMA) Applied to Protein Conformational Flexibility

(2015) Elisa Frezza et al.   Journal of Chemical Theory and Computation

Exploring Free Energy Landscapes of Large Conformational Changes: Molecular Dynamics with Excited Normal Modes

(2015) Mauricio G. S. Costa et al.   Journal of Chemical Theory and Computation

Conformational ensembles and sampled energy landscapes: Analysis and comparison

(2015) Frédéric Cazals et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

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

Integrative, dynamic structural biology at atomic resolution—it's about time

(2015) Henry van den Bedem et al.   NATURE METHODS

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

SPECTRUS: A Dimensionality Reduction Approach for Identifying Dynamical Domains in Protein Complexes from Limited Structural Datasets

(2015) Luca Ponzoni et al.   STRUCTURE

Localized reconstruction of subunits from electron cryomicroscopy images of macromolecular complexes

(2015) Serban L. Ilca et al.   Nature Communications

Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways

(2015) Sean L. Seyler et al.   PLoS Computational Biology

A local-optimization refinement algorithm in single particle analysis for macromolecular complex with multiple rigid modules

(2015) Hong Shan et al.   Protein & Cell

Sampling the conformational space of the catalytic subunit of human γ-secretase

(2015) Xiao-chen Bai et al.   eLife

Diffusion maps, clustering and fuzzy Markov modeling in peptide folding transitions

(2014) Lilia V. Nedialkova et al.   JOURNAL OF CHEMICAL PHYSICS

Hybrid Electron Microscopy Normal Mode Analysis graphical interface and protocol

(2014) Carlos Oscar S. Sorzano 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

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

(2014) Qiyu Jin et al.   STRUCTURE

Combined Quantum Mechanics/Molecular Mechanics (QM/MM) Methods in Computational Enzymology

(2013) Marc W. van der Kamp et al.   BIOCHEMISTRY

Global Transitions of Proteins Explored by a Multiscale Hybrid Methodology: Application to Adenylate Kinase

(2013) Mert Gur et al.   BIOPHYSICAL JOURNAL

Normal mode analysis based on an elastic network model for biomolecules in the Protein Data Bank, which uses dihedral angles as independent variables

(2013) Hiroshi Wako et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

Likelihood-based classification of cryo-EM images using FREALIGN

(2013) Dmitry Lyumkis et al.   JOURNAL OF STRUCTURAL BIOLOGY

The power of coarse graining in biomolecular simulations

(2013) Helgi I. Ingólfsson et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Biomolecular Simulation: A Computational Microscope for Molecular Biology

(2012) Ron O. Dror et al.   Annual Review of Biophysics

Dynamics in cryo EM reconstructions visualized with maximum-likelihood derived variance maps

(2012) Qiu Wang et al.   JOURNAL OF STRUCTURAL BIOLOGY

Three-dimensional reconstruction of the statistics of heterogeneous objects from a collection of one projection image of each object

(2012) Yili Zheng et al.   JOURNAL OF THE OPTICAL SOCIETY OF AMERICA A-OPTICS IMAGE SCIENCE AND VISION

On developing coarse-grained models for biomolecular simulation: a review

(2012) Sereina Riniker et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

iMod: multipurpose normal mode analysis in internal coordinates

(2011) José Ramón Lopéz-Blanco et al.   BIOINFORMATICS

Ligand-induced conformational change of a protein reproduced by a linear combination of displacement vectors obtained from normal mode analysis

(2011) Hiroshi Wako et al.   BIOPHYSICAL CHEMISTRY

Force-momentum-based self-guided Langevin dynamics: A rapid sampling method that approaches the canonical ensemble

(2011) Xiongwu Wu et al.   JOURNAL OF CHEMICAL PHYSICS

Determination of reaction coordinates via locally scaled diffusion map

(2011) Mary A. Rohrdanz et al.   JOURNAL OF CHEMICAL PHYSICS

Subtle Monte Carlo Updates in Dense Molecular Systems

(2011) Sandro Bottaro et al.   Journal of Chemical Theory and Computation

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

Instantaneous Normal Modes as an Unforced Reaction Coordinate for Protein Conformational Transitions

(2010) Cheng Peng et al.   BIOPHYSICAL JOURNAL

Harmonic Vibrational Analysis in Delocalized Internal Coordinates

(2010) Frank Jensen et al.   Journal of Chemical Theory and Computation

A clustering approach to multireference alignment of single-particle projections in electron microscopy

(2010) C.O.S. Sorzano et al.   JOURNAL OF STRUCTURAL BIOLOGY

Torsional Network Model: Normal Modes in Torsion Angle Space Better Correlate with Conformation Changes in Proteins

(2010) Raul Mendez et al.   PHYSICAL REVIEW LETTERS

An Approach for De Novo Structure Determination of Dynamic Molecular Assemblies by Electron Cryomicroscopy

(2010) Bjoern Sander et al.   STRUCTURE

QM/MM Methods for Biomolecular Systems

(2009) Hans Martin Senn et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Normal Mode Analysis of Biomolecular Structures: Functional Mechanisms of Membrane Proteins

(2009) Ivet Bahar et al.   CHEMICAL REVIEWS

Exploring conformational modes of macromolecular assemblies by multiparticle cryo-EM

(2009) Christian MT Spahn et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Allosteric Transitions of Supramolecular Systems Explored by Network Models: Application to Chaperonin GroEL

(2009) Zheng Yang et al.   PLoS Computational Biology

Brownian Dynamics Simulations of a Wild Type and Mutants of Bovine Pancreatic Trypsin Inhibitors

(2008) Akifumi Oda et al.   BIOLOGICAL & PHARMACEUTICAL BULLETIN

Mechanism of Signal Propagation upon Retinal Isomerization: Insights from Molecular Dynamics Simulations of Rhodopsin Restrained by Normal Modes

(2008) Basak Isin et al.   BIOPHYSICAL JOURNAL

Multiple Subunit Fitting into a Low-Resolution Density Map of a Macromolecular Complex Using a Gaussian Mixture Model

(2008) Takeshi Kawabata   BIOPHYSICAL JOURNAL

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation

Comparisons of experimental and computed protein anisotropic temperature factors

(2008) Lei Yang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Heterogeneity of Large Macromolecular Complexes Revealed by 3D Cryo-EM Variance Analysis

(2008) Wei Zhang et al.   STRUCTURE