Dynamic properties of force fields

Markov state models of biomolecular conformational dynamics

(2014) John D Chodera et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Thermodynamics of Deca-alanine Folding in Water

(2014) Anthony Hazel et al.   Journal of Chemical Theory and Computation

Optimizing Potentials for a Liquid Mixture: A New Force Field for a tert-Butanol and Water Solution

(2014) Michele Di Pierro et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Complex RNA Folding Kinetics Revealed by Single-Molecule FRET and Hidden Markov Models

(2014) Bettina G. Keller et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Dynamic neutron scattering from conformational dynamics. II. Application using molecular dynamics simulation and Markov modeling

(2013) Zheng Yi et al.   JOURNAL OF CHEMICAL PHYSICS

Dynamic neutron scattering from conformational dynamics. I. Theory and Markov models

(2013) Benjamin Lindner et al.   JOURNAL OF CHEMICAL PHYSICS

Projected and hidden Markov models for calculating kinetics and metastable states of complex molecules

(2013) Frank Noé et al.   JOURNAL OF CHEMICAL PHYSICS

Performance of Different Force Fields in Force Probe Simulations

(2013) Thomas Schlesier et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Non-Exponential Kinetics and a Complete Folding Pathway of an α-Helical Heteropeptide: Direct Observation and Comprehensive Molecular Dynamics

(2013) Gouri S. Jas et al.   JOURNAL OF PHYSICAL CHEMISTRY B

NMR Relaxation in Proteins with Fast Internal Motions and Slow Conformational Exchange: Model-Free Framework and Markov State Simulations

(2013) Junchao Xia et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements

(2012) Kyle A. Beauchamp 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

Critical Assessment of Current Force Fields. Short Peptide Test Case

(2012) Jiří Vymětal et al.   Journal of Chemical Theory and Computation

The intrinsic conformational features of amino acids from a protein coil library and their applications in force field development

(2012) Fan Jiang et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Systematic Validation of Protein Force Fields against Experimental Data

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

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

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

(2011) Stefano Piana et al.   BIOPHYSICAL JOURNAL

Markov models and dynamical fingerprints: Unraveling the complexity of molecular kinetics

(2011) Bettina G. Keller et al.   CHEMICAL PHYSICS

Multiple state transition interface sampling of alanine dipeptide in explicit solvent

(2011) Wei-Na Du et al.   JOURNAL OF CHEMICAL PHYSICS

Dynamical reweighting: Improved estimates of dynamical properties from simulations at multiple temperatures

(2011) John D. Chodera et al.   JOURNAL OF CHEMICAL PHYSICS

Optimal use of data in parallel tempering simulations for the construction of discrete-state Markov models of biomolecular dynamics

(2011) Jan-Hendrik Prinz et al.   JOURNAL OF CHEMICAL PHYSICS

Markov models of molecular kinetics: Generation and validation

(2011) Jan-Hendrik Prinz et al.   JOURNAL OF CHEMICAL PHYSICS

An Analysis of the Validity of Markov State Models for Emulating the Dynamics of Classical Molecular Systems and Ensembles

(2011) Bettina Keller et al.   Journal of Chemical Theory and Computation

Simulating the T-Jump-Triggered Unfolding Dynamics of trpzip2 Peptide and Its Time-Resolved IR and Two-Dimensional IR Signals Using the Markov State Model Approach

(2011) Wei Zhuang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Markov State Model Reveals Folding and Functional Dynamics in Ultra-Long MD Trajectories

(2011) Thomas J. Lane et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Dynamical fingerprints for probing individual relaxation processes in biomolecular dynamics with simulations and kinetic experiments

(2011) F. Noe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Complex Folding Network of Single Calmodulin Molecules

(2011) J. Stigler et al.   SCIENCE

How Fast-Folding Proteins Fold

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

Single-molecule fluorescence spectroscopy maps the folding landscape of a large protein

(2011) Menahem Pirchi et al.   Nature Communications

Scrutinizing Molecular Mechanics Force Fields on the Submicrosecond Timescale with NMR Data

(2010) Oliver F. Lange et al.   BIOPHYSICAL JOURNAL

Influence of Side Chain Conformations on Local Conformational Features of Amino Acids and Implication for Force Field Development

(2010) Fan Jiang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

On the Approximation Quality of Markov State Models

(2010) Marco Sarich et al.   MULTISCALE MODELING & SIMULATION

What stabilizes the 314-helix in β3-peptides? A conformational analysis using molecular simulation

(2010) Bettina Keller et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

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

Atomic-Level Characterization of the Structural Dynamics of Proteins

(2010) D. E. Shaw et al.   SCIENCE

Force Field Bias in Protein Folding Simulations

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

Long-timescale molecular dynamics simulations of protein structure and function

(2009) John L Klepeis et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

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

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

Are Current Molecular Dynamics Force Fields too Helical?

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

Coarse Master Equations for Peptide Folding Dynamics†

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