Computational biophysics meets cryo‐EM revolution in the search for the functional dynamics of biomolecular systems

Conformational space exploration of cryo-EM structures by variability refinement

(2023) Pavel V. Afonine et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Estimating conformational landscapes from Cryo-EM particles by 3D Zernike polynomials

(2023) D. Herreros et al.   Nature Communications

Critical mechanistic features of HIV-1 viral capsid assembly

(2023) Manish Gupta et al.   Science Advances

Steps of actin filament branch formation by Arp2/3 complex investigated with coarse-grained molecular dynamics

(2023) Shuting Zhang et al.   Frontiers in Cell and Developmental Biology

Deep learning for reconstructing protein structures from cryo-EM density maps: Recent advances and future directions

(2023) Nabin Giri et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

(2023) Muyuan Chen et al.   JOURNAL OF MOLECULAR BIOLOGY

Methods for Cryo-EM Single Particle Reconstruction of Macromolecules Having Continuous Heterogeneity

(2023) Bogdan Toader et al.   JOURNAL OF MOLECULAR BIOLOGY

CryoFold 2.0: Cryo-EM Structure Determination with MELD

(2023) Liwei Chang et al.   Journal of Physical Chemistry A

Ensemble Reweighting Using Cryo-EM Particle Images

(2023) Wai Shing Tang et al.   Journal of Physical Chemistry B

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

(2023) Ali Punjani et al.   NATURE METHODS

Scipion Flexibility Hub: an integrative framework for advanced analysis of conformational heterogeneity in cryoEM

(2023) D. Herreros et al.   Acta Crystallographica Section D-Structural Biology

Conformational heterogeneity and probability distributions from single-particle cryo-electron microscopy

(2023) Wai Shing Tang et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Time-resolved cryo-EM using a combination of droplet microfluidics with on-demand jetting

(2023) Stefania Torino et al.   NATURE METHODS

Structural and functional insight into regulation of kinesin-1 by microtubule-associated protein MAP7

(2022) Luke S. Ferro et al.   SCIENCE

Sampling of Protein Conformational Space Using Hybrid Simulations: A Critical Assessment of Recent Methods

(2022) Burak T. Kaynak et al.   Frontiers in Molecular Biosciences

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

On bias, variance, overfitting, gold standard and consensus in single-particle analysis by cryo-electron microscopy

(2022) C. O. S. Sorzano et al.   Acta Crystallographica Section D-Structural Biology

Protein dynamics developments for the large scale and cryoEM: case study of ProDy 2.0

(2022) James Michael Krieger et al.   Acta Crystallographica Section D-Structural Biology

Emerging Themes in CryoEM─Single Particle Analysis Image Processing

(2022) Jose Luis Vilas et al.   CHEMICAL REVIEWS

Structural dynamics: review of time-resolved cryo-EM

(2022) Märt-Erik Mäeots et al.   Acta Crystallographica Section D-Structural Biology

Exploring TRPC3 Interaction with Cholesterol through Coarse-Grained Molecular Dynamics Simulations

(2022) Amy Clarke et al.   Biomolecules

Molecular Insights into the Misfolding and Dimerization Dynamics of the Full-Length α-Synuclein from Atomistic Discrete Molecular Dynamics Simulations

(2022) Yu Zhang et al.   ACS Chemical Neuroscience

Cooperative antimicrobial action of melittin on lipid membranes: A coarse-grained molecular dynamics study

(2022) Yusuke Miyazaki et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Improved AlphaFold modeling with implicit experimental information

(2022) Thomas C. Terwilliger et al.   NATURE METHODS

StarMap: a user-friendly workflow for Rosetta-driven molecular structure refinement

(2022) Wolfgang Lugmayr et al.   Nature Protocols

Putting AlphaFold models to work with phenix.process_predicted_model and ISOLDE

(2022) Robert D. Oeffner et al.   Acta Crystallographica Section D-Structural 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

Artificial Intelligence in Cryo-Electron Microscopy

(2022) Jeong Min Chung et al.   Life-Basel

Mutually beneficial confluence of structure-based modeling of protein dynamics and machine learning methods

(2022) Anupam Banerjee et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

(2022) Mohamad Harastani et al.   JOURNAL OF STRUCTURAL BIOLOGY

Deep generative modeling for volume reconstruction in cryo-electron microscopy

(2022) Claire Donnat et al.   JOURNAL OF STRUCTURAL BIOLOGY

Breathing and Tilting: Mesoscale Simulations Illuminate Influenza Glycoprotein Vulnerabilities

(2022) Lorenzo Casalino et al.   ACS Central Science

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

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

ProDy 2.0: Increased Scale and Scope after 10 Years of Protein Dynamics Modelling with Python

(2021) She Zhang et al.   BIOINFORMATICS

Critical Interactions Between the SARS-CoV-2 Spike Glycoprotein and the Human ACE2 Receptor

(2021) Elhan Taka et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

ClustENMD: Efficient sampling of biomolecular conformational space at atomic resolution

(2021) Burak T Kaynak et al.   BIOINFORMATICS

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

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

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

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

(2021) Muyuan Chen et al.   NATURE METHODS

A Bayesian approach to extracting free-energy profiles from cryo-electron microscopy experiments

(2021) Julian Giraldo-Barreto et al.   Scientific Reports

Insights into the substrate binding mechanism of SULT1A1 through molecular dynamics with excited normal modes simulations

(2021) Balint Dudas et al.   Scientific Reports

Probing allosteric regulations with coevolution-driven molecular simulations

(2021) Francesco Colizzi et al.   Science Advances

Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems

(2021) Adam Liwo et al.   Biomolecules

Challenges and triumphs in cryo-electron tomography

(2021) Ryan K. Hylton et al.   iScience

Cryo-EM single-particle structure refinement and map calculation using Servalcat

(2021) Keitaro Yamashita et al.   Acta Crystallographica Section D-Structural Biology

A New Strategy for Atomic Flexible Fitting in Cryo-EM Maps by Molecular Dynamics with Excited Normal Modes (MDeNM-EMfit)

(2020) Mauricio G. S. Costa et al.   Journal of Chemical Information and Modeling

Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly

(2020) Robert A. Dick et al.   PLoS Pathogens

Mesoscale All-Atom Influenza Virus Simulations Suggest New Substrate Binding Mechanism

(2020) Jacob D. Durrant et al.   ACS Central Science

Towards gaining sight of multiscale events: utilizing network models and normal modes in hybrid methods

(2020) James M Krieger et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

A review of advancements in coarse-grained molecular dynamics simulations

(2020) Soumil Y. Joshi et al.   MOLECULAR SIMULATION

State-dependent sequential allostery exhibited by chaperonin TRiC/CCT revealed by network analysis of Cryo-EM maps

(2020) Yan Zhang et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

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

(2020) Beata Turoňová et al.   SCIENCE

Beyond Shielding: The Roles of Glycans in the SARS-CoV-2 Spike Protein

(2020) Lorenzo Casalino et al.   ACS Central Science

Adaptability and specificity: how do proteins balance opposing needs to achieve function?

(2020) Bentley Wingert et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Conformational ensemble of native α-synuclein in solution as determined by short-distance crosslinking constraint-guided discrete molecular dynamics simulations

(2019) Nicholas I. Brodie et al.   PLoS Computational Biology

Directionality of dynein is controlled by the angle and length of its stalk

(2019) Sinan Can et al.   NATURE

Automated cryo-EM structure refinement using correlation-driven molecular dynamics

(2019) Maxim Igaev et al.   eLife

Enhanced sampling in molecular dynamics

(2019) Yi Isaac Yang et al.   JOURNAL OF CHEMICAL PHYSICS

Pre‐ and post‐docking sampling of conformational changes using ClustENM and HADDOCK for protein‐protein and protein‐DNA systems

(2019) Zeynep Kurkcuoglu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Deriving and refining atomic models in crystallography and cryo-EM: the latest Phenix tools to facilitate structure analysis

(2019) Bruno P. Klaholz   Acta Crystallographica Section D-Structural Biology

Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix

(2019) Dorothee Liebschner et al.   Acta Crystallographica Section D-Structural Biology

Hybrid Electron Microscopy Normal Mode Analysis with Scipion

(2019) Mohamad Harastani et al.   PROTEIN SCIENCE

Machine learning for protein folding and dynamics

(2019) Frank Noé et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Intrinsic dynamics is evolutionarily optimized to enable allosteric behavior

(2019) Yan Zhang et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Simultaneous Determination of Protein Structure and Dynamics Using Cryo-Electron Microscopy

(2018) Massimiliano Bonomi et al.   BIOPHYSICAL JOURNAL

Protein structure-based drug design: from docking to molecular dynamics

(2018) Paweł Śledź et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Gaussian-input Gaussian mixture model for representing density maps and atomic models

(2018) Takeshi Kawabata   JOURNAL OF STRUCTURAL BIOLOGY

ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps

(2018) Tristan Ian Croll   Acta Crystallographica Section D-Structural Biology

Constructing atomic structural models into cryo-EM densities using molecular dynamics – Pros and cons

(2018) Yuhang Wang et al.   JOURNAL OF STRUCTURAL BIOLOGY

Molecular Dynamics Simulation for All

(2018) Scott A. Hollingsworth et al.   NEURON

Single-particle cryo-EM—How did it get here and where will it go

(2018) Yifan Cheng   SCIENCE

An inter‐dimer allosteric switch controls NMDA receptor activity

(2018) Jean‐Baptiste Esmenjaud et al.   EMBO JOURNAL

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

Finite Mixture Models

(2018) Geoffrey J. McLachlan et al.   Annual Review of Statistics and Its Application

Determination of protein structural ensembles using cryo-electron microscopy

(2018) Massimiliano Bonomi et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

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

Effect of Dimerization on the Dynamics of Neurotransmitter:Sodium Symporters

(2017) Mert Gur et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Solving protein structures using short-distance cross-linking constraints as a guide for discrete molecular dynamics simulations

(2017) Nicholas I. Brodie et al.   Science Advances

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

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

Coarse-Grained Protein Models and Their Applications

(2016) Sebastian Kmiecik et al.   CHEMICAL REVIEWS

New generation of elastic network models

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

Multiscale simulation of DNA

(2016) Pablo D Dans 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

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

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

CHARMM-GUI MDFF/xMDFF Utilizer for Molecular Dynamics Flexible Fitting Simulations in Various Environments

(2016) Yifei Qi et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

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

Ligand Docking to Intermediate and Close-To-Bound Conformers Generated by an Elastic Network Model Based Algorithm for Highly Flexible Proteins

(2016) Zeynep Kurkcuoglu et al.   PLoS One

The structure and flexibility of conical HIV-1 capsids determined within intact virions

(2016) Simone Mattei et al.   SCIENCE

Prediction and validation of protein intermediate states from structurally rich ensembles and coarse-grained simulations

(2016) Laura Orellana et al.   Nature Communications

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

(2016) Slavica Jonić et al.   Biomed Research International

Molecular dynamics-based refinement and validation for sub-5 Å cryo-electron microscopy maps

(2016) Abhishek Singharoy et al.   eLife

Metainference: A Bayesian inference method for heterogeneous systems

(2016) M. Bonomi et al.   Science Advances

Metadynamic metainference: Enhanced sampling of the metainference ensemble using metadynamics

(2016) Massimiliano Bonomi et al.   Scientific Reports

The anisotropic network model web server at 2015 (ANM 2.0)

(2015) E. Eyal et al.   BIOINFORMATICS

Omokage search: shape similarity search service for biomolecular structures in both the PDB and EMDB

(2015) Hirofumi Suzuki et al.   BIOINFORMATICS

Adaptability of protein structures to enable functional interactions and evolutionary implications

(2015) Turkan Haliloglu et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Energy landscape of LeuT from molecular simulations

(2015) Mert Gur et al.   JOURNAL OF CHEMICAL PHYSICS

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

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

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

The revolution will not be crystallized: a new method sweeps through structural biology

(2015) Ewen Callaway   NATURE

EMDataBank unified data resource for 3DEM

(2015) Catherine L. Lawson et al.   NUCLEIC ACIDS RESEARCH

The Adaptive Biasing Force Method: Everything You Always Wanted To Know but Were Afraid To Ask

(2014) Jeffrey Comer et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

Structural modeling from electron microscopy data

(2014) José Ramón López-Blanco et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Exploring the Conformational Transitions of Biomolecular Systems Using a Simple Two-State Anisotropic Network Model

(2014) Avisek Das et al.   PLoS Computational Biology

Exploration of conformational transition pathways from coarse-grained simulations

(2013) Pedro Sfriso et al.   BIOINFORMATICS

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

(2013) Mert Gur et al.   BIOPHYSICAL JOURNAL

Global motions exhibited by proteins in micro- to milliseconds simulations concur with anisotropic network model predictions

(2013) M. Gur et al.   JOURNAL OF CHEMICAL PHYSICS

iMODFIT: Efficient and robust flexible fitting based on vibrational analysis in internal coordinates

(2013) José Ramón Lopéz-Blanco et al.   JOURNAL OF STRUCTURAL BIOLOGY

Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics

(2013) Gongpu Zhao et al.   NATURE

High-Resolution Comparative Modeling with RosettaCM

(2013) Yifan Song et al.   STRUCTURE

Finding Conformational Transition Pathways from Discrete Molecular Dynamics Simulations

(2012) Pedro Sfriso et al.   Journal of Chemical Theory and Computation

Elastic Network Models Are Robust to Variations in Formalism

(2012) Nicholas Leioatts et al.   Journal of Chemical Theory and Computation

Fitting Multimeric Protein Complexes into Electron Microscopy Maps Using 3D Zernike Descriptors

(2012) Juan Esquivel-Rodríguez et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Multiscale natural moves refine macromolecules using single-particle electron microscopy projection images

(2012) J. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Using Enhanced Sampling and Structural Restraints to Refine Atomic Structures into Low-Resolution Electron Microscopy Maps

(2012) Harish Vashisth et al.   STRUCTURE

Modelling dynamics in protein crystal structures by ensemble refinement

(2012) B Tom Burnley et al.   eLife

REFMAC5 for the refinement of macromolecular crystal structures

(2011) Garib N. Murshudov et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

ProDy: Protein Dynamics Inferred from Theory and Experiments

(2011) A. Bakan et al.   BIOINFORMATICS

Accurate Flexible Fitting of High-Resolution Protein Structures into Cryo-Electron Microscopy Maps Using Coarse-Grained Pseudo-Energy Minimization

(2011) Wenjun Zheng   BIOPHYSICAL JOURNAL

Excited states of ribosome translocation revealed through integrative molecular modeling

(2011) P. C. Whitford et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Umbrella sampling

(2011) Johannes Kästner   Wiley Interdisciplinary Reviews-Computational Molecular Science

Cooperative dynamics of proteins unraveled by network models

(2011) Eran Eyal et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Discrete molecular dynamics

(2011) Elizabeth A. Proctor et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Metadynamics

(2011) Alessandro Barducci et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

PHENIX: a comprehensive Python-based system for macromolecular structure solution

(2010) Paul D. Adams et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Global Dynamics of Proteins: Bridging Between Structure and Function

(2010) Ivet Bahar et al.   Annual Review of Biophysics

Elucidation of Amyloid β-Protein Oligomerization Mechanisms: Discrete Molecular Dynamics Study

(2010) B. Urbanc et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Consensus modes, a robust description of protein collective motions from multiple-minima normal mode analysis—application to the HIV-1 protease

(2010) Paulo Ricardo Batista et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Validating and improving elastic network models with molecular dynamics simulations

(2010) Tod D. Romo et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

(2009) Ivet Bahar et al.   CHEMICAL REVIEWS

Refinement of Protein Structures into Low-Resolution Density Maps Using Rosetta

(2009) Frank DiMaio et al.   JOURNAL OF MOLECULAR BIOLOGY

The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding

(2009) A. Bakan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conformational Transition Pathways Explored by Monte Carlo Simulation Integrated with Collective Modes

(2008) Nigar Kantarci-Carsibasi et al.   BIOPHYSICAL JOURNAL

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

(2008) Marek Orzechowski et al.   BIOPHYSICAL JOURNAL

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

Collective motions in Glucosamine-6-phosphate Synthase: Influence of Ligand Binding and role in Ammonia Channelling and Opening of the Fructose-6-Phosphate Binding Site

(2008) Nicolas Floquet et al.   JOURNAL OF MOLECULAR BIOLOGY

Ab initio RNA folding by discrete molecular dynamics: From structure prediction to folding mechanisms

(2008) F. Ding et al.   RNA

Protein Structure Fitting and Refinement Guided by Cryo-EM Density

(2008) Maya Topf et al.   STRUCTURE

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

(2008) Leonardo G. Trabuco et al.   STRUCTURE