Combining Experiments and Simulations Using the Maximum Entropy Principle

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

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

Inference of Structure Ensembles of Flexible Biomolecules from Sparse, Averaged Data

(2013) Simon Olsson et al.   PLoS One

Stimulus-dependent Maximum Entropy Models of Neural Population Codes

(2013) Einat Granot-Atedgi et al.   PLoS Computational Biology

On the Use of Experimental Observations to Bias Simulated Ensembles

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

Systematic Parametrization of Polarizable Force Fields from Quantum Chemistry Data

(2012) Lee-Ping Wang et al.   Journal of Chemical Theory and Computation

Efficient sampling of protein conformational space using fast loop building and batch minimization on highly parallel computers

(2012) Michael D. Tyka et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

A New Multiscale Algorithm and Its Application to Coarse-Grained Peptide Models for Self-Assembly

(2012) Scott P. Carmichael et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Will molecular dynamics simulations of proteins ever reach equilibrium?

(2012) Samuel Genheden et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Systematic Validation of Protein Force Fields against Experimental Data

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

Modelling dynamics in protein crystal structures by ensemble refinement

(2012) B Tom Burnley et al.   eLife

Transmembrane Helix Orientation and Dynamics: Insights from Ensemble Dynamics with Solid-State NMR Observables

(2011) Sunhwan Jo et al.   BIOPHYSICAL JOURNAL

Generative probabilistic models extend the scope of inferential structure determination

(2011) Simon Olsson et al.   JOURNAL OF MAGNETIC RESONANCE

Direct-coupling analysis of residue coevolution captures native contacts across many protein families

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

SAXS Ensemble Refinement of ESCRT-III CHMP3 Conformational Transitions

(2011) Bartosz Różycki et al.   STRUCTURE

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

Similarity Measures for Protein Ensembles

(2009) Kresten Lindorff-Larsen et al.   PLoS One

Maximum Entropy Reconstructions of Dynamic Signaling Networks from Quantitative Proteomics Data

(2009) Jason W. Locasale et al.   PLoS One

Molecular simulation as an aid to experimentalists

(2008) Wilfred F van Gunsteren et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Recognition Dynamics Up to Microseconds Revealed from an RDC-Derived Ubiquitin Ensemble in Solution

(2008) O. F. Lange et al.   SCIENCE

Experimental Parameterization of an Energy Function for the Simulation of Unfolded Proteins

(2007) Anders B. Norgaard et al.   BIOPHYSICAL JOURNAL