X-ray refinement significantly underestimates the level of microscopic heterogeneity in biomolecular crystals

Peptide Crystal Simulations Reveal Hidden Dynamics

(2013) Pawel A. Janowski et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Vienna-PTM web server: a toolkit for MD simulations of protein post-translational modifications

(2013) Christian Margreitter et al.   NUCLEIC ACIDS RESEARCH

A Systematic Framework for Molecular Dynamics Simulations of Protein Post-Translational Modifications

(2013) Drazen Petrov et al.   PLoS Computational Biology

Biomolecular Simulation: A Computational Microscope for Molecular Biology

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

The future of the protein data bank

(2012) Helen M. Berman et al.   BIOPOLYMERS

On the Contribution of Linear Correlations to Quasi-harmonic Conformational Entropy in Proteins

(2012) Anton A. Polyansky et al.   Journal of Chemical Theory and Computation

Modelling dynamics in protein crystal structures by ensemble refinement

(2012) B Tom Burnley et al.   eLife

Using molecular-dynamics simulations to understand and improve the treatment of anharmonic vibrations. I. Study of positional parameters

(2011) Anthony M. Reilly et al.   ACTA CRYSTALLOGRAPHICA SECTION A

Using molecular-dynamics simulations to understand and improve the treatment of anharmonic vibrations. II. Developing and assessing new Debye–Waller factors

(2011) Anthony M. Reilly et al.   ACTA CRYSTALLOGRAPHICA SECTION A

REFMAC5 for the refinement of macromolecular crystal structures

(2011) Garib N. Murshudov et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Overview of theCCP4 suite and current developments

(2011) Martyn D. Winn et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

MSMBuilder2: Modeling Conformational Dynamics on the Picosecond to Millisecond Scale

(2011) Kyle A. Beauchamp et al.   Journal of Chemical Theory and Computation

Dynamics May Significantly Influence the Estimation of Interatomic Distances in Biomolecular X-ray Structures

(2011) Antonija Kuzmanic et al.   JOURNAL OF MOLECULAR BIOLOGY

Microscopic Analysis of Protein Oxidative Damage: Effect of Carbonylation on Structure, Dynamics, and Aggregability of Villin Headpiece

(2011) Drazen Petrov et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

PHENIX: a comprehensive Python-based system for macromolecular structure solution

(2010) Paul D. Adams et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Determination of Ensemble-Average Pairwise Root Mean-Square Deviation from Experimental B-Factors

(2010) Antonija Kuzmanic et al.   BIOPHYSICAL JOURNAL

Simulations of a Protein Crystal with a High Resolution X-ray Structure: Evaluation of Force Fields and Water Models

(2010) David S. Cerutti et al.   JOURNAL OF PHYSICAL CHEMISTRY B

All-Atom Contact Model for Understanding Protein Dynamics from Crystallographic B-Factors

(2009) Da-Wei Li et al.   BIOPHYSICAL JOURNAL

Dynamics of the Streptavidin−Biotin Complex in Solution and in Its Crystal Lattice: Distinct Behavior Revealed by Molecular Simulations

(2009) David S. Cerutti et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Conformational averaging in structural biology: issues, challenges and computational solutions

(2009) Daniela Kruschel et al.   Molecular BioSystems

Determination of Protein Structures—A Series of Fortunate Events

(2008) Maksymilian Chruszcz et al.   BIOPHYSICAL JOURNAL

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation

On the relationship between the protein structure and protein dynamics

(2008) Chih-Hao Lu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS