Combining enhanced sampling with experiment-directed simulation of the GYG peptide

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

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

A Direct Method for Incorporating Experimental Data into Multiscale Coarse-Grained Models

(2016) Thomas Dannenhoffer-Lafage et al.   Journal of Chemical Theory and Computation

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

Enhanced sampling techniques in molecular dynamics simulations of biological systems

(2015) Rafael C. Bernardi et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Enhanced sampling techniques in biomolecular simulations

(2015) Vojtech Spiwok et al.   BIOTECHNOLOGY ADVANCES

Designing Free Energy Surfaces That Match Experimental Data with Metadynamics

(2015) Andrew D. White et al.   Journal of Chemical Theory and Computation

pH-dependent random coil 1H, 13C, and 15N chemical shifts of the ionizable amino acids: a guide for protein pK a measurements

(2014) Gerald Platzer et al.   JOURNAL OF BIOMOLECULAR NMR

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

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

Replica-Averaged Metadynamics

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

Restrained-Ensemble Molecular Dynamics Simulations Based on Distance Histograms from Double Electron–Electron Resonance Spectroscopy

(2013) Benoît Roux et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Hamiltonian replica exchange in GROMACS: a flexible implementation

(2013) Giovanni Bussi   MOLECULAR PHYSICS

On the Use of Experimental Observations to Bias Simulated Ensembles

(2012) Jed W. Pitera et al.   Journal of Chemical Theory and Computation

Efficient Simulation of Explicitly Solvated Proteins in the Well-Tempered Ensemble

(2012) Michael Deighan et al.   Journal of Chemical Theory and Computation

Development of the CHARMM Force Field for Lipids

(2011) R. W. Pastor et al.   Journal of Physical Chemistry Letters

Enhanced Sampling in the Well-Tempered Ensemble

(2010) M. Bonomi et al.   PHYSICAL REVIEW LETTERS

Using NMR Chemical Shifts as Structural Restraints in Molecular Dynamics Simulations of Proteins

(2010) Paul Robustelli et al.   STRUCTURE

Neighbor-Dependent Ramachandran Probability Distributions of Amino Acids Developed from a Hierarchical Dirichlet Process Model

(2010) Daniel Ting et al.   PLoS Computational Biology

Fast and Accurate Predictions of Protein NMR Chemical Shifts from Interatomic Distances

(2009) Kai J. Kohlhoff et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Adaptive biasing force method for scalar and vector free energy calculations

(2008) Eric Darve et al.   JOURNAL OF CHEMICAL PHYSICS

Make Life Simple: Unleash the Full Power of the Parallel Tempering Algorithm

(2008) Elmar Bittner et al.   PHYSICAL REVIEW LETTERS

Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method

(2008) Alessandro Barducci et al.   PHYSICAL REVIEW LETTERS

Common Interruptions in the Repeating Tripeptide Sequence of Non-fibrillar Collagens: Sequence Analysis and Structural Studies on Triple-helix Peptide Models

(2007) Geetha Thiagarajan et al.   JOURNAL OF MOLECULAR BIOLOGY