Ensemble Reweighting Using Cryo-EM Particle Images

Size-and-Shape Space Gaussian Mixture Models for Structural Clustering of Molecular Dynamics Trajectories

(2022) Heidi Klem et al.   Journal of Chemical Theory and Computation

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

Reweighting methods for elucidation of conformation ensembles of proteins

(2022) Raquel Gama Lima Costa et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Efficient Flexible Fitting Refinement with Automatic Error Fixing for De Novo Structure Modeling from Cryo-EM Density Maps

(2021) Takaharu Mori et al.   Journal of Chemical Information and Modeling

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

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

Fast and eager k-medoids clustering: O(k) runtime improvement of the PAM, CLARA, and CLARANS algorithms

(2021) Erich Schubert et al.   INFORMATION SYSTEMS

Energy landscape of domain motion in glutamate dehydrogenase deduced from cryo‐electron microscopy

(2020) Mao Oide et al.   FEBS Journal

Single-Particle Cryo-Electron Microscopy: Mathematical Theory, Computational Challenges, and Opportunities

(2020) Tamir Bendory et al.   IEEE SIGNAL PROCESSING MAGAZINE

Macromolecular modeling and design in Rosetta: recent methods and frameworks

(2020) Julia Koehler Leman et al.   NATURE METHODS

Single-particle cryo-EM at atomic resolution

(2020) Takanori Nakane et al.   NATURE

Retrieving functional pathways of biomolecules from single-particle snapshots

(2020) Ali Dashti et al.   Nature Communications

Efficient Ensemble Refinement by Reweighting

(2019) Jürgen Köfinger et al.   Journal of Chemical Theory and Computation

Coupling Molecular Dynamics and Deep Learning to Mine Protein Conformational Space

(2019) Matteo T. Degiacomi   STRUCTURE

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

(2019) Maxim Igaev et al.   eLife

Boltzmann generators: Sampling equilibrium states of many-body systems with deep learning

(2019) Frank Noé et al.   SCIENCE

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

(2018) Massimiliano Bonomi et al.   BIOPHYSICAL JOURNAL

Likelihood-based structural analysis of electron microscopy images

(2018) Pilar Cossio et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Biophysical experiments and biomolecular simulations: A perfect match?

(2018) Sandro Bottaro et al.   SCIENCE

Stan: A Probabilistic Programming Language

(2017) Bob Carpenter et al.   Journal of Statistical Software

Metainference: A Bayesian inference method for heterogeneous systems

(2016) M. Bonomi et al.   Science Advances

Bayesian ensemble refinement by replica simulations and reweighting

(2015) Gerhard Hummer et al.   JOURNAL OF CHEMICAL PHYSICS

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

The Resolution Revolution

(2014) W. Kuhlbrandt   SCIENCE

Combining Experiments and Simulations Using the Maximum Entropy Principle

(2014) Wouter Boomsma et al.   PLoS Computational Biology

On the statistical equivalence of restrained-ensemble simulations with the maximum entropy method

(2013) Benoît Roux et al.   JOURNAL OF CHEMICAL PHYSICS

Bayesian analysis of individual electron microscopy images: Towards structures of dynamic and heterogeneous biomolecular assemblies

(2013) Pilar Cossio et al.   JOURNAL OF STRUCTURAL BIOLOGY

Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM

(2013) Xueming Li et al.   NATURE METHODS

Integrative Structural Biology

(2013) A. B. Ward et al.   SCIENCE

How Robust Are Protein Folding Simulations with Respect to Force Field Parameterization?

(2011) Stefano Piana et al.   BIOPHYSICAL JOURNAL

How Fast-Folding Proteins Fold

(2011) K. Lindorff-Larsen et al.   SCIENCE

SAXS Ensemble Refinement of ESCRT-III CHMP3 Conformational Transitions

(2011) Bartosz Różycki et al.   STRUCTURE

Ribosome dynamics and tRNA movement by time-resolved electron cryomicroscopy

(2010) Niels Fischer et al.   NATURE

Improved side-chain torsion potentials for the Amber ff99SB protein force field

(2010) Kresten Lindorff-Larsen et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Molecular dynamics flexible fitting: A practical guide to combine cryo-electron microscopy and X-ray crystallography

(2009) Leonardo G. Trabuco et al.   METHODS

Macromolecular Modeling with Rosetta

(2008) Rhiju Das et al.   Annual Review of Biochemistry