A theoretical view of protein dynamics

X-ray refinement significantly underestimates the level of microscopic heterogeneity in biomolecular crystals

(2014) Antonija Kuzmanic et al.   Nature Communications

Connecting Protein Conformational Dynamics with Catalytic Function As Illustrated in Dihydrofolate Reductase

(2013) Yao Fan et al.   BIOCHEMISTRY

Exploration of conformational transition pathways from coarse-grained simulations

(2013) Pedro Sfriso et al.   BIOINFORMATICS

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

(2013) Sander Pronk et al.   BIOINFORMATICS

Molecular Mechanism of SSR128129E, an Extracellularly Acting, Small-Molecule, Allosteric Inhibitor of FGF Receptor Signaling

(2013) Corentin Herbert et al.   CANCER CELL

Architecture and Membrane Interactions of the EGF Receptor

(2013) Anton Arkhipov et al.   CELL

Perspective on the Martini model

(2013) Siewert J. Marrink et al.   CHEMICAL SOCIETY REVIEWS

Coarse-grain modelling of protein–protein interactions

(2013) Marc Baaden et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Automated Force Field Parameterization for Nonpolarizable and Polarizable Atomic Models Based on Ab Initio Target Data

(2013) Lei Huang et al.   Journal of Chemical Theory and Computation

The Theory of Ultra-Coarse-Graining. 1. General Principles

(2013) James F. Dama et al.   Journal of Chemical Theory and Computation

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald

(2013) Romelia Salomon-Ferrer et al.   Journal of Chemical Theory and Computation

Picomolar Inhibitors of HIV Reverse Transcriptase Featuring Bicyclic Replacement of a Cyanovinylphenyl Group

(2013) Won-Gil Lee et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Native States of Fast-Folding Proteins Are Kinetic Traps

(2013) Alex Dickson et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Emergence of Glass-like Behavior in Markov State Models of Protein Folding Dynamics

(2013) Jeffrey K. Weber et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Evidence for Cardiolipin Binding Sites on the Membrane-Exposed Surface of the Cytochrome bc1

(2013) Clement Arnarez et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

(2013) Gongpu Zhao et al.   NATURE

Recovery from slow inactivation in K+ channels is controlled by water molecules

(2013) Jared Ostmeyer et al.   NATURE

Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways

(2013) Kai J. Kohlhoff et al.   Nature Chemistry

Energy barriers and driving forces in tRNA translocation through the ribosome

(2013) Lars V Bock et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Coevolutionary signals across protein lineages help capture multiple protein conformations

(2013) F. Morcos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phosphate release coupled to rotary motion of F1-ATPase

(2013) K.-i. Okazaki et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Toward an atomistic description of the urea-denatured state of proteins

(2013) M. Candotti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Native contacts determine protein folding mechanisms in atomistic simulations

(2013) R. B. Best et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Atomic-level description of ubiquitin folding

(2013) S. Piana et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Using Ligand-Mapping Simulations to Design a Ligand Selectively Targeting a Cryptic Surface Pocket of Polo-Like Kinase 1

(2012) Yaw Sing Tan et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Biomolecular Simulation: A Computational Microscope for Molecular Biology

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

Three-Dimensional Structures of Membrane Proteins from Genomic Sequencing

(2012) Thomas A. Hopf et al.   CELL

In silico FRET from simulated dye dynamics

(2012) Martin Hoefling et al.   COMPUTER PHYSICS COMMUNICATIONS

Atomistic molecular simulations of protein folding

(2012) Robert B Best   CURRENT OPINION IN STRUCTURAL BIOLOGY

PaLaCe: A Coarse-Grain Protein Model for Studying Mechanical Properties

(2012) Marco Pasi et al.   Journal of Chemical Theory and Computation

Application of Drug-Perturbed Essential Dynamics/Molecular Dynamics (ED/MD) to Virtual Screening and Rational Drug Design

(2012) Rima Chaudhuri et al.   Journal of Chemical Theory and Computation

Fast Atomistic Molecular Dynamics Simulations from Essential Dynamics Samplings

(2012) Oliver Carrillo et al.   Journal of Chemical Theory and Computation

Finding Conformational Transition Pathways from Discrete Molecular Dynamics Simulations

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

Consistent View of Protein Fluctuations from All-Atom Molecular Dynamics and Coarse-Grained Dynamics with Knowledge-Based Force-Field

(2012) Michal Jamroz et al.   Journal of Chemical Theory and Computation

Characterization of a Dynamic String Method for the Construction of Transition Pathways in Molecular Reactions

(2012) Margaret E. Johnson et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Multilevel X-Pol: A Fragment-Based Method with Mixed Quantum Mechanical Representations of Different Fragments

(2012) Yingjie Wang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Structure of the TatC core of the twin-arginine protein transport system

(2012) Sarah E. Rollauer et al.   NATURE

KOSMOS: a universal morph server for nucleic acids, proteins and their complexes

(2012) S. Seo et al.   NUCLEIC ACIDS RESEARCH

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

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

Comparing proteins by their internal dynamics: Exploring structure–function relationships beyond static structural alignments

(2012) Cristian Micheletti   Physics of Life Reviews

Exploring Protein Dynamics Space: The Dynasome as the Missing Link between Protein Structure and Function

(2012) Ulf Hensen et al.   PLoS One

Kinetic characterization of the critical step in HIV-1 protease maturation

(2012) S. K. Sadiq et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Simple few-state models reveal hidden complexity in protein folding

(2012) K. A. Beauchamp et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular driving forces defining lipid positions around aquaporin-0

(2012) C. Aponte-Santamaria et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein folding kinetics and thermodynamics from atomistic simulation

(2012) S. Piana et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mechanism of Voltage Gating in Potassium Channels

(2012) M. O. Jensen et al.   SCIENCE

New advances in metadynamics

(2012) Ludovico Sutto et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Synergistic use of NMR and MD simulations to study the structural heterogeneity of proteins

(2012) Santiago Esteban-Martín et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

A Preformed Binding Interface in the Unbound Ensemble of an Intrinsically Disordered Protein: Evidence from Molecular Simulations

(2012) Michael Knott et al.   PLoS Computational Biology

Virus Capsid Dissolution Studied by Microsecond Molecular Dynamics Simulations

(2012) Daniel S. D. Larsson et al.   PLoS Computational Biology

Coarse-Grained (Multiscale) Simulations in Studies of Biophysical and Chemical Systems

(2011) Shina C.L. Kamerlin et al.   Annual Review of Physical Chemistry

iMod: multipurpose normal mode analysis in internal coordinates

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

Optimized Torsion-Angle Normal Modes Reproduce Conformational Changes More Accurately Than Cartesian Modes

(2011) Jenelle K. Bray et al.   BIOPHYSICAL JOURNAL

Computationally-Guided Optimization of a Docking Hit to Yield Catechol Diethers as Potent Anti-HIV Agents

(2011) Mariela Bollini et al.   JOURNAL OF MEDICINAL CHEMISTRY

Weak Long-Range Correlated Motions in a Surface Patch of Ubiquitin Involved in Molecular Recognition

(2011) R. Bryn Fenwick et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The Native Ensemble and Folding of a Protein Molten-Globule: Functional Consequence of Downhill Folding

(2011) Athi N. Naganathan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Unsuspected pathway of the allosteric transition in hemoglobin

(2011) S. Fischer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiscale simulations suggest a mechanism for integrin inside-out activation

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

Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations

(2011) I. Buch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

How Fast-Folding Proteins Fold

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

A Systematic Study of the Energetics Involved in Structural Changes upon Association and Connectivity in Protein Interaction Networks

(2011) Amelie Stein et al.   STRUCTURE

Polarization effects in molecular interactions

(2011) F. Javier Luque et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

The empirical valence bond model: theory and applications

(2011) Shina C. L. Kamerlin 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

NMR-Based Protein Potentials

(2010) Da-Wei Li et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Anharmonic Normal Mode Analysis of Elastic Network Model Improves the Modeling of Atomic Fluctuations in Protein Crystal Structures

(2010) Wenjun Zheng   BIOPHYSICAL JOURNAL

High-Throughput All-Atom Molecular Dynamics Simulations Using Distributed Computing

(2010) I. Buch et al.   Journal of Chemical Information and Modeling

Approaching Elastic Network Models to Molecular Dynamics Flexibility

(2010) Laura Orellana et al.   Journal of Chemical Theory and Computation

Refinement of Ensembles Describing Unstructured Proteins Using NMR Residual Dipolar Couplings

(2010) Santi Esteban-Martín et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Changes in Transmembrane Helix Alignment by Arginine Residues Revealed by Solid-State NMR Experiments and Coarse-Grained MD Simulations

(2010) Vitaly V. Vostrikov et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Everything you wanted to know about Markov State Models but were afraid to ask

(2010) Vijay S. Pande et al.   METHODS

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

(2010) Raul Mendez et al.   PHYSICAL REVIEW LETTERS

Conformational selection in the molten globule state of the nuclear coactivator binding domain of CBP

(2010) Magnus Kjaergaard et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Principles of protein folding - A perspective from simple exact models

(2010) Ken A. Dill et al.   PROTEIN SCIENCE

Atomic-Level Characterization of the Structural Dynamics of Proteins

(2010) D. E. Shaw et al.   SCIENCE

MoDEL (Molecular Dynamics Extended Library): A Database of Atomistic Molecular Dynamics Trajectories

(2010) Tim Meyer et al.   STRUCTURE

Multiscale Coarse-Graining of the Protein Energy Landscape

(2010) Ronald D. Hills et al.   PLoS Computational Biology

QM/MM Methods for Biomolecular Systems

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

FlexServ: an integrated tool for the analysis of protein flexibility

(2009) J. Camps et al.   BIOINFORMATICS

A Self-Consistent Description of the Conformational Behavior of Chemically Denatured Proteins from NMR and Small Angle Scattering

(2009) Pau Bernadó et al.   BIOPHYSICAL JOURNAL

Evaluating the Performance of the ff99SB Force Field Based on NMR Scalar Coupling Data

(2009) Lauren Wickstrom et al.   BIOPHYSICAL JOURNAL

Allosteric Transitions in Biological Nanomachines are Described by Robust Normal Modes of Elastic Networks

(2009) Wenjun Zheng et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

Simulated Tempering Distributed Replica Sampling, Virtual Replica Exchange, and Other Generalized-Ensemble Methods for Conformational Sampling

(2009) Sarah Rauscher et al.   Journal of Chemical Theory and Computation

ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale

(2009) M. J. Harvey et al.   Journal of Chemical Theory and Computation

X-Pol Potential: An Electronic Structure-Based Force Field for Molecular Dynamics Simulation of a Solvated Protein in Water

(2009) Wangshen Xie et al.   Journal of Chemical Theory and Computation

Explicit Polarization (X-Pol) Potential Using ab Initio Molecular Orbital Theory and Density Functional Theory†

(2009) Lingchun Song et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations

(2009) Frank Noé et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

StoneHinge: Hinge prediction by network analysis of individual protein structures

(2009) Kevin S. Keating et al.   PROTEIN SCIENCE

Molecular modeling and dynamics studies with explicit inclusion of electronic polarizability: theory and applications

(2009) Pedro E. M. Lopes et al.   THEORETICAL CHEMISTRY ACCOUNTS

Comparison of molecular dynamics and superfamily spaces of protein domain deformation

(2009) Javier A Velazquez-Muriel et al.   BMC STRUCTURAL BIOLOGY

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

(2009) Zheng Yang et al.   PLoS Computational Biology

Exploring the Suitability of Coarse-Grained Techniques for the Representation of Protein Dynamics

(2008) Agustí Emperador et al.   BIOPHYSICAL JOURNAL

Function and structure of inherently disordered proteins

(2008) A Keith Dunker et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

United-Atom Discrete Molecular Dynamics of Proteins Using Physics-Based Potentials

(2008) Agustí Emperador et al.   Journal of Chemical Theory and Computation

The MARTINI Coarse-Grained Force Field: Extension to Proteins

(2008) Luca Monticelli et al.   Journal of Chemical Theory and Computation

Target Flexibility: An Emerging Consideration in Drug Discovery and Design†

(2008) Pietro Cozzini et al.   JOURNAL OF MEDICINAL CHEMISTRY

Coarse Master Equations for Peptide Folding Dynamics†

(2008) Nicolae-Viorel Buchete et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Insights into protein flexibility: The relationship between normal modes and conformational change upon protein-protein docking

(2008) S. E. Dobbins et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamical roles of metal ions and the disulfide bond in Cu, Zn superoxide dismutase folding and aggregation

(2008) F. Ding et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Large-Scale Molecular Dynamics Simulations of Self-Assembling Systems

(2008) M. L. Klein et al.   SCIENCE

Structural Biology by NMR: Structure, Dynamics, and Interactions

(2008) Phineus R. L. Markwick et al.   PLoS Computational Biology

Coarse-grained models of protein folding: toy models or predictive tools?

(2007) Cecilia Clementi   CURRENT OPINION IN STRUCTURAL BIOLOGY