Challenges in protein-folding simulations

Comparing geometric and kinetic cluster algorithms for molecular simulation data

(2010) Bettina Keller et al.   JOURNAL OF CHEMICAL PHYSICS

A Survey of λ Repressor Fragments from Two-State to Downhill Folding

(2010) Feng Liu et al.   JOURNAL OF MOLECULAR BIOLOGY

Current Status of the AMOEBA Polarizable Force Field

(2010) Jay W. Ponder et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Going beyond Clustering in MD Trajectory Analysis: An Application to Villin Headpiece Folding

(2010) Aruna Rajan et al.   PLoS One

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

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

Force Field Bias in Protein Folding Simulations

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

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

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

Identification of the protein folding transition state from molecular dynamics trajectories

(2009) S. Muff et al.   JOURNAL OF CHEMICAL PHYSICS

Polarizable Intermolecular Potentials for Water and Benzene Interacting with Halide and Metal Ions

(2009) Fabien Archambault 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

Quantum Chemistry on Graphical Processing Units. 3. Analytical Energy Gradients, Geometry Optimization, and First Principles Molecular Dynamics

(2009) Ivan S. Ufimtsev et al.   Journal of Chemical Theory and Computation

Quantum Chemistry on Graphical Processing Units. 2. Direct Self-Consistent-Field Implementation

(2009) Ivan S. Ufimtsev et al.   Journal of Chemical Theory and Computation

Accelerating molecular dynamic simulation on graphics processing units

(2009) Mark S. Friedrichs et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Computations of Standard Binding Free Energies with Molecular Dynamics Simulations

(2009) Yuqing Deng et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

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

Probing the Folding Transition State Structure of the Villin Headpiece Subdomain via Side Chain and Backbone Mutagenesis

(2009) Michelle R. Bunagan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Detection of a Transient Intermediate in a Rapid Protein Folding Process by Solid-State Nuclear Magnetic Resonance

(2009) Kan-Nian Hu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Interpeptide interactions induce helix to strand structural transition in Aβ peptides

(2009) Takako Takeda et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Rate Constant and Reaction Coordinate of Trp-Cage Folding in Explicit Water

(2008) Jarek Juraszek et al.   BIOPHYSICAL JOURNAL

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

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

Are Current Molecular Dynamics Force Fields too Helical?

(2008) Robert B. Best et al.   BIOPHYSICAL JOURNAL

The fast-folding HP35 double mutant has a substantially reduced primary folding free energy barrier

(2008) Hongxing Lei 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

One-Dimensional Barrier-Preserving Free-Energy Projections of a β-sheet Miniprotein: New Insights into the Folding Process

(2008) Sergei V. Krivov et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Computing the stability diagram of the Trp-cage miniprotein

(2008) D. Paschek et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Universality and diversity of folding mechanics for three-helix bundle proteins

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

Diffusive reaction dynamics on invariant free energy profiles

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

Revisiting the Carboxylic Acid Dimers in Aqueous Solution:  Interplay of Hydrogen Bonding, Hydrophobic Interactions, and Entropy†

(2007) Jianhan Chen et al.   JOURNAL OF PHYSICAL CHEMISTRY B