An implementation of the maximum-caliber principle by replica-averaged time-resolved restrained simulations

Communication: Introducing prescribed biases in out-of-equilibrium Markov models

(2018) Purushottam D. Dixit   JOURNAL OF CHEMICAL PHYSICS

Perspective: Maximum caliber is a general variational principle for dynamical systems

(2018) Purushottam D. Dixit et al.   JOURNAL OF CHEMICAL PHYSICS

Caliber Corrected Markov Modeling (C2M2): Correcting Equilibrium Markov Models

(2018) Purushottam D. Dixit et al.   Journal of Chemical Theory and Computation

Markov State Models: From an Art to a Science

(2018) Brooke E. Husic et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

RNA force field with accuracy comparable to state-of-the-art protein force fields

(2018) Dazhi Tan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Communication: Improved ab initio molecular dynamics by minimally biasing with experimental data

(2017) Andrew D. White et al.   JOURNAL OF CHEMICAL PHYSICS

Metadynamic metainference: Convergence towards force field independent structural ensembles of a disordered peptide

(2017) Thomas Löhr et al.   JOURNAL OF CHEMICAL PHYSICS

Coarse-Grained Directed Simulation

(2017) Glen M. Hocky et al.   Journal of Chemical Theory and Computation

Combining experimental and simulation data of molecular processes via augmented Markov models

(2017) Simon Olsson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Combining Simulations and Solution Experiments as a Paradigm for RNA Force Field Refinement

(2016) Andrea Cesari et al.   Journal of Chemical Theory and Computation

A Maximum-Caliber Approach to Predicting Perturbed Folding Kinetics Due to Mutations

(2016) Hongbin Wan et al.   Journal of Chemical Theory and Computation

Spectral gap optimization of order parameters for sampling complex molecular systems

(2016) Pratyush Tiwary et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metainference: A Bayesian inference method for heterogeneous systems

(2016) M. Bonomi et al.   Science Advances

Metadynamic metainference: Enhanced sampling of the metainference ensemble using metadynamics

(2016) Massimiliano Bonomi et al.   Scientific Reports

Communication: Maximum caliber is a general variational principle for nonequilibrium statistical mechanics

(2015) Michael J. Hazoglou et al.   JOURNAL OF CHEMICAL PHYSICS

Dynamic properties of force fields

(2015) F. Vitalini et al.   JOURNAL OF CHEMICAL PHYSICS

Bayesian ensemble refinement by replica simulations and reweighting

(2015) Gerhard Hummer et al.   JOURNAL OF CHEMICAL PHYSICS

Comparing Molecular Dynamics Force Fields in the Essential Subspace

(2015) Fernando Martín-García et al.   PLoS One

Measuring the Hydrogen/Deuterium Exchange of Proteins at High Spatial Resolution by Mass Spectrometry: Overcoming Gas-Phase Hydrogen/Deuterium Scrambling

(2014) Kasper D. Rand et al.   ACCOUNTS OF CHEMICAL RESEARCH

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

Efficient and Minimal Method to Bias Molecular Simulations with Experimental Data

(2014) Andrew D. White et al.   Journal of Chemical Theory and Computation

Combining Experiments and Simulations Using the Maximum Entropy Principle

(2014) Wouter Boomsma et al.   PLoS Computational Biology

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

(2013) Sander Pronk et al.   BIOINFORMATICS

PLUMED 2: New feathers for an old bird

(2013) Gareth A. Tribello et al.   COMPUTER PHYSICS COMMUNICATIONS

On the statistical equivalence of restrained-ensemble simulations with the maximum entropy method

(2013) Benoît Roux et al.   JOURNAL OF CHEMICAL PHYSICS

Molecular dynamics simulations with replica-averaged structural restraints generate structural ensembles according to the maximum entropy principle

(2013) Andrea Cavalli et al.   JOURNAL OF CHEMICAL PHYSICS

Identification of slow molecular order parameters for Markov model construction

(2013) Guillermo Pérez-Hernández et al.   JOURNAL OF CHEMICAL PHYSICS

Replica-Averaged Metadynamics

(2013) Carlo Camilloni et al.   Journal of Chemical Theory and Computation

Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9

(2013) Christian R. Schwantes et al.   Journal of Chemical Theory and Computation

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

Principles of maximum entropy and maximum caliber in statistical physics

(2013) Steve Pressé et al.   REVIEWS OF MODERN PHYSICS

Biomolecular Simulation: A Computational Microscope for Molecular Biology

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

On the Use of Experimental Observations to Bias Simulated Ensembles

(2012) Jed W. Pitera 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

Characterization of the Conformational Equilibrium between the Two Major Substates of RNase A Using NMR Chemical Shifts

(2012) Carlo Camilloni et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Systematic Validation of Protein Force Fields against Experimental Data

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

Equilibrium Sampling in Biomolecular Simulations

(2011) Daniel M. Zuckerman   Annual Review of Biophysics

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

(2011) Stefano Piana et al.   BIOPHYSICAL JOURNAL

Time resolved SAXS and RNA folding

(2011) Lois Pollack   BIOPOLYMERS

Modeling Stochastic Dynamics in Biochemical Systems with Feedback Using Maximum Caliber

(2011) S. Pressé et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Maximum Caliber: A variational approach applied to two-state dynamics

(2008) Gerhard Stock et al.   JOURNAL OF CHEMICAL PHYSICS

Tracking the structural dynamics of proteins in solution using time-resolved wide-angle X-ray scattering

(2008) Marco Cammarata et al.   NATURE METHODS

An all-atom structure-based potential for proteins: Bridging minimal models with all-atom empirical forcefields

(2008) Paul C. Whitford et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Stochastic Actions for Diffusive Dynamics:  Reweighting, Sampling, and Minimization†

(2007) Artur B. Adib   JOURNAL OF PHYSICAL CHEMISTRY B