ENCORE: Software for Quantitative Ensemble Comparison

Comparing Molecular Dynamics Force Fields in the Essential Subspace

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

Bayesian Energy Landscape Tilting: Towards Concordant Models of Molecular Ensembles

(2014) Kyle A. Beauchamp et al.   BIOPHYSICAL JOURNAL

E pluribus unum, no more: from one crystal, many conformations

(2014) Rahel A Woldeyes et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Markov state models of biomolecular conformational dynamics

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

Surprisal Metrics for Quantifying Perturbed Conformational Dynamics in Markov State Models

(2014) Vincent A. Voelz et al.   Journal of Chemical Theory and Computation

Improved Cross Validation of a Static Ubiquitin Structure Derived from High Precision Residual Dipolar Couplings Measured in a Drug-Based Liquid Crystalline Phase

(2014) Alexander S. Maltsev et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Measuring similarity between dynamic ensembles of biomolecules

(2014) Shan Yang et al.   NATURE METHODS

Combining Experiments and Simulations Using the Maximum Entropy Principle

(2014) Wouter Boomsma et al.   PLoS Computational Biology

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

Predicting the Thermodynamics and Kinetics of Helix Formation in a Cyclic Peptide Model

(2013) João M. Damas et al.   Journal of Chemical Theory and Computation

Comprehensive macromolecular conformations mapped by quantitative SAXS analyses

(2013) Greg L Hura et al.   NATURE METHODS

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

(2013) Simon Olsson et al.   PLoS One

Phosphorylation Drives a Dynamic Switch in Serine/Arginine-Rich Proteins

(2013) ShengQi Xiang et al.   STRUCTURE

Quantitative Comparison of Conformational Ensembles

(2012) Kevin C. Wolfe et al.   Entropy

Determination of structural fluctuations of proteins from structure-based calculations of residual dipolar couplings

(2012) Rinaldo W. Montalvao et al.   JOURNAL OF BIOMOLECULAR NMR

Comparing Conformational Ensembles Using the Kullback–Leibler Divergence Expansion

(2012) Christopher L. McClendon et al.   Journal of Chemical Theory and Computation

On the Use of Experimental Observations to Bias Simulated Ensembles

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

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

Fast large-scale clustering of protein structures using Gauss integrals

(2011) Tim Harder et al.   BIOINFORMATICS

MDAnalysis: A toolkit for the analysis of molecular dynamics simulations

(2011) Naveen Michaud-Agrawal et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Let’s get honest about sampling

(2011) David L. Mobley   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Weak Long-Range Correlated Motions in a Surface Patch of Ubiquitin Involved in Molecular Recognition

(2011) R. Bryn Fenwick et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Tree preserving embedding

(2011) A. D. Shieh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

How Fast-Folding Proteins Fold

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

Cython: The Best of Both Worlds

(2010) Stefan Behnel et al.   COMPUTING IN SCIENCE & ENGINEERING

Fast Mapping of Global Protein Folding States by Multivariate NMR: A GPS for Proteins

(2010) Anders Malmendal et al.   PLoS One

Atomic-Level Characterization of the Structural Dynamics of Proteins

(2010) D. E. Shaw et al.   SCIENCE

Similarity Measures for Protein Ensembles

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

Mixture models for protein structure ensembles

(2008) M. Hirsch et al.   BIOINFORMATICS

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

(2008) O. F. Lange et al.   SCIENCE