Accelerated molecular dynamics simulations of protein folding

Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations

(2014) Stefano Piana et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation

(2014) Yinglong Miao et al.   Journal of Chemical Theory and Computation

Achieving Rigorous Accelerated Conformational Sampling in Explicit Solvent

(2014) Urmi Doshi et al.   Journal of Physical Chemistry Letters

Folding Simulations for Proteins with Diverse Topologies Are Accessible in Days with a Physics-Based Force Field and Implicit Solvent

(2014) Hai Nguyen et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Folding kinetics of WW domains with the united residue force field for bridging microscopic motions and experimental measurements

(2014) Rui Zhou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural Insights into the Trp-Cage Folding Intermediate Formation

(2013) Petra Rovó et al.   CHEMISTRY-A EUROPEAN JOURNAL

High-Resolution Free-Energy Landscape Analysis of α-Helical Protein Folding: HP35 and Its Double Mutant

(2013) Polina V. Banushkina 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

How Kinetics within the Unfolded State Affects Protein Folding: An Analysis Based on Markov State Models and an Ultra-Long MD Trajectory

(2013) Nan-jie Deng et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Population Based Reweighting of Scaled Molecular Dynamics

(2013) William Sinko et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Folding Dynamics of the Trp-Cage Miniprotein: Evidence for a Native-Like Intermediate from Combined Time-Resolved Vibrational Spectroscopy and Molecular Dynamics Simulations

(2013) Heleen Meuzelaar et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Characterization of the free-energy landscapes of proteins by NMR-guided metadynamics

(2013) D. Granata et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Atomic-level description of ubiquitin folding

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

Force-Field Dependence of Chignolin Folding and Misfolding: Comparison with Experiment and Redesign

(2012) Petra Kührová et al.   BIOPHYSICAL JOURNAL

SPFP: Speed without compromise—A mixed precision model for GPU accelerated molecular dynamics simulations

(2012) Scott Le Grand et al.   COMPUTER PHYSICS COMMUNICATIONS

Atomistic molecular simulations of protein folding

(2012) Robert B Best   CURRENT OPINION IN STRUCTURAL BIOLOGY

To milliseconds and beyond: challenges in the simulation of protein folding

(2012) Thomas J Lane et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Improved Statistical Sampling and Accuracy with Accelerated Molecular Dynamics on Rotatable Torsions

(2012) Urmi Doshi et al.   Journal of Chemical Theory and Computation

Comparison of Secondary Structure Formation Using 10 Different Force Fields in Microsecond Molecular Dynamics Simulations

(2012) Elio A. Cino et al.   Journal of Chemical Theory and Computation

Routine Access to Millisecond Time Scale Events with Accelerated Molecular Dynamics

(2012) Levi C.T. Pierce et al.   Journal of Chemical Theory and Computation

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born

(2012) Andreas W. Götz et al.   Journal of Chemical Theory and Computation

Systematic Validation of Protein Force Fields against Experimental Data

(2012) Kresten Lindorff-Larsen et al.   PLoS One

Allosteric networks in thrombin distinguish procoagulant vs. anticoagulant activities

(2012) P. M. Gasper et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nucleotide-dependent mechanism of Get3 as elucidated from free energy calculations

(2012) J. Wereszczynski 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

β-hairpin forms by rolling up from C-terminal: Topological guidance of early folding dynamics

(2012) Søren Enemark et al.   Scientific Reports

An overview of the Amber biomolecular simulation package

(2012) Romelia Salomon-Ferrer et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

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

(2011) Stefano Piana et al.   BIOPHYSICAL JOURNAL

Architecture, implementation and parallelisation of the GROMOS software for biomolecular simulation

(2011) Nathan Schmid et al.   COMPUTER PHYSICS COMMUNICATIONS

Accelerating chemical reactions: Exploring reactive free-energy surfaces using acceleratedab initiomolecular dynamics

(2011) Levi C. T. Pierce et al.   JOURNAL OF CHEMICAL PHYSICS

Enhanced Lipid Diffusion and Mixing in Accelerated Molecular Dynamics

(2011) Yi Wang et al.   Journal of Chemical Theory and Computation

The Fast-Folding Mechanism of Villin Headpiece Subdomain Studied by Multiscale Distributed Computing

(2011) Ryuhei Harada et al.   Journal of Chemical Theory and Computation

Validation of the GROMOS 54A7 Force Field with Respect to β-Peptide Folding

(2011) Wei Huang et al.   Journal of Chemical Theory and Computation

Adaptive Accelerated Molecular Dynamics (Ad-AMD) Revealing the Molecular Plasticity of P450cam

(2011) Phineus R. L. Markwick et al.   Journal of Physical Chemistry Letters

Studying functional dynamics in bio-molecules using accelerated molecular dynamics

(2011) Phineus R. L. Markwick et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Quantitative comparison of villin headpiece subdomain simulations and triplet-triplet energy transfer experiments

(2011) K. A. Beauchamp 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

Recent developments and applications of the CHARMM force fields

(2011) Xiao Zhu et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Accessing a Hidden Conformation of the Maltose Binding Protein Using Accelerated Molecular Dynamics

(2011) Denis Bucher et al.   PLoS Computational Biology

Tackling Force-Field Bias in Protein Folding Simulations: Folding of Villin HP35 and Pin WW Domains in Explicit Water

(2010) Jeetain Mittal et al.   BIOPHYSICAL JOURNAL

An unlocking/relocking barrier in conformational fluctuations of villin headpiece subdomain

(2010) A. Reiner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Fip35 WW Domain Folds with Structural and Mechanistic Heterogeneity in Molecular Dynamics Simulations

(2009) Daniel L. Ensign et al.   BIOPHYSICAL JOURNAL

Common Structural Transitions in Explicit-Solvent Simulations of Villin Headpiece Folding

(2009) Peter L. Freddolino et al.   BIOPHYSICAL JOURNAL

Optimized Molecular Dynamics Force Fields Applied to the Helix−Coil Transition of Polypeptides

(2009) Robert B. Best et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A Kinetic Model of Trp-Cage Folding from Multiple Biased Molecular Dynamics Simulations

(2009) Fabrizio Marinelli et al.   PLoS Computational Biology

Ten-Microsecond Molecular Dynamics Simulation of a Fast-Folding WW Domain

(2008) Peter L. Freddolino et al.   BIOPHYSICAL JOURNAL

A statistical analysis of the precision of reweighting-based simulations

(2008) Tongye Shen et al.   JOURNAL OF CHEMICAL PHYSICS

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

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

The Trp-cage: optimizing the stability of a globular miniprotein

(2008) B. Barua et al.   PROTEIN ENGINEERING DESIGN & SELECTION