Generalized correlation-based dynamical network analysis: a new high-performance approach for identifying allosteric communications in molecular dynamics trajectories

Machine learning approaches for analyzing and enhancing molecular dynamics simulations

(2020) Yihang Wang et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Streptavidin/biotin: Tethering geometry defines unbinding mechanics

(2020) Steffen M. Sedlak et al.   Science Advances

Scalable molecular dynamics on CPU and GPU architectures with NAMD

(2020) James C. Phillips et al.   JOURNAL OF CHEMICAL PHYSICS

High force catch bond mechanism of bacterial adhesion in the human gut

(2020) Zhaowei Liu et al.   Nature Communications

Symmetry, Rigidity, and Allosteric Signaling: From Monomeric Proteins to Molecular Machines

(2019) D. Thirumalai et al.   CHEMICAL REVIEWS

Characterization of Lipid–Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation

(2019) Melanie P. Muller et al.   CHEMICAL REVIEWS

Graph dynamical networks for unsupervised learning of atomic scale dynamics in materials

(2019) Tian Xie et al.   Nature Communications

Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism

(2019) Abhishek Singharoy et al.   CELL

NAMD goes quantum: an integrative suite for hybrid simulations

(2018) Marcelo C R Melo et al.   NATURE METHODS

Molecular mechanism of extreme mechanostability in a pathogen adhesin

(2018) Lukas F. Milles et al.   SCIENCE

Direction Matters: Monovalent Streptavidin/Biotin Complex under Load

(2018) Steffen M. Sedlak et al.   NANO LETTERS

Eigenvector centrality for characterization of protein allosteric pathways

(2018) Christian F. A. Negre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Combining in Vitro and in Silico Single-Molecule Force Spectroscopy to Characterize and Tune Cellulosomal Scaffoldin Mechanics

(2017) Tobias Verdorfer et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Networks of Dynamic Allostery Regulate Enzyme Function

(2017) Michael Joseph Holliday et al.   STRUCTURE

Machine Learning and Network Analysis of Molecular Dynamics Trajectories Reveal Two Chains of Red/Ox-specific Residue Interactions in Human Protein Disulfide Isomerase

(2017) Razieh Karamzadeh et al.   Scientific Reports

Skeletal Dysplasia Mutations Effect on Human Filamins’ Structure and Mechanosensing

(2017) Jonne Seppälä et al.   Scientific Reports

Computational approaches to detect allosteric pathways in transmembrane molecular machines

(2016) Sebastian Stolzenberg et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

HTMD: High-Throughput Molecular Dynamics for Molecular Discovery

(2016) S. Doerr et al.   Journal of Chemical Theory and Computation

QwikMD — Integrative Molecular Dynamics Toolkit for Novices and Experts

(2016) João V. Ribeiro et al.   Scientific Reports

A Comparative Analysis of Community Detection Algorithms on Artificial Networks

(2016) Zhao Yang et al.   Scientific Reports

Enhanced sampling techniques in molecular dynamics simulations of biological systems

(2015) Rafael C. Bernardi et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Allostery without a conformational change? Revisiting the paradigm

(2015) Ruth Nussinov et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Molecular dynamics simulations of large macromolecular complexes

(2015) Juan R Perilla et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Mapping Mechanical Force Propagation through Biomolecular Complexes

(2015) Constantin Schoeler et al.   NANO LETTERS

Redox-induced activation of the proton pump in the respiratory complex I

(2015) Vivek Sharma et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Computational approaches to mapping allosteric pathways

(2014) Victoria A Feher et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Weighted Implementation of Suboptimal Paths (WISP): An Optimized Algorithm and Tool for Dynamical Network Analysis

(2014) Adam T. Van Wart et al.   Journal of Chemical Theory and Computation

The ensemble nature of allostery

(2014) Hesam N. Motlagh et al.   NATURE

Mutual Information between Discrete and Continuous Data Sets

(2014) Brian C. Ross   PLoS One

Electrostatics, hydration, and proton transfer dynamics in the membrane domain of respiratory complex I

(2014) V. R. I. Kaila et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structures of mitochondrial oxidative phosphorylation supercomplexes and mechanisms for their stabilisation

(2013) Yuriy Chaban et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

Allostery in Disease and in Drug Discovery

(2013) Ruth Nussinov et al.   CELL

Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration

(2013) Cameron Abrams et al.   Entropy

Crystal structure of the entire respiratory complex I

(2013) Rozbeh Baradaran et al.   NATURE

Activation and dynamic network of the M2 muscarinic receptor

(2013) Y. Miao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

NetworkView: 3D display and analysis of protein{middle dot}RNA interaction networks

(2012) J. Eargle et al.   BIOINFORMATICS

Hybrid QM/MM Molecular Dynamics Study of Benzocaine in a Membrane Environment: How Does a Quantum Mechanical Treatment of Both Anesthetic and Lipids Affect Their Interaction

(2012) Rafael C. Bernardi et al.   Journal of Chemical Theory and Computation

Exploring Residue Component Contributions to Dynamical Network Models of Allostery

(2012) Adam T. VanWart et al.   Journal of Chemical Theory and Computation

Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ1 and χ2 Dihedral Angles

(2012) Robert B. Best et al.   Journal of Chemical Theory and Computation

Structural dynamics of the aminoacylation and proofreading functional cycle of bacterial leucyl-tRNA synthetase

(2012) Andrés Palencia et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Automated 3D structure composition for large RNAs

(2012) Mariusz Popenda et al.   NUCLEIC ACIDS RESEARCH

The Structural Dynamics of the Flavivirus Fusion Peptide–Membrane Interaction

(2012) Ygara S. Mendes et al.   PLoS One

Allosteric pathways in imidazole glycerol phosphate synthase

(2012) I. Rivalta et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural Basis for Allosteric Regulation of GPCRs by Sodium Ions

(2012) W. Liu et al.   SCIENCE

Conformational and functional analysis of molecular dynamics trajectories by Self-Organising Maps

(2011) Domenico Fraccalvieri et al.   BMC BIOINFORMATICS

MDAnalysis: A toolkit for the analysis of molecular dynamics simulations

(2011) Naveen Michaud-Agrawal et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Dynamical behaviour of the human β1-adrenoceptor under agonist binding

(2011) Lucas V.B. Hoelz et al.   MOLECULAR SIMULATION

The role of helices 5 and 6 on the human β1-adrenoceptor activation mechanism

(2011) Lucas V.B. Hoelz et al.   MOLECULAR SIMULATION

Cython: The Best of Both Worlds

(2010) Stefan Behnel et al.   COMPUTING IN SCIENCE & ENGINEERING

The architecture of respiratory complex I

(2010) Rouslan G. Efremov et al.   NATURE

Experimental and computational determination of tRNA dynamics

(2009) Rebecca W. Alexander et al.   FEBS LETTERS

Dynamical networks in tRNA:protein complexes

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

Distinguishing influence-based contagion from homophily-driven diffusion in dynamic networks

(2009) S. Aral et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Allostery: Absence of a Change in Shape Does Not Imply that Allostery Is Not at Play

(2008) Chung-Jung Tsai et al.   JOURNAL OF MOLECULAR BIOLOGY

Fast unfolding of communities in large networks

(2008) Vincent D Blondel et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

Allostery and cooperativity revisited

(2008) Qiang Cui et al.   PROTEIN SCIENCE