Molecular dynamics simulation of triclinic lysozyme in a crystal lattice

All-atom crystal simulations of DNA and RNA duplexes

(2015) Chunmei Liu et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

The R-factor gap in macromolecular crystallography: an untapped potential for insights on accurate structures

(2014) James M. Holton et al.   FEBS Journal

ff14ipq: A Self-Consistent Force Field for Condensed-Phase Simulations of Proteins

(2014) David S. Cerutti et al.   Journal of Chemical Theory and Computation

Aligning Experimental and Theoretical Anisotropic B-Factors: Water Models, Normal-Mode Analysis Methods, and Metrics

(2014) Lei Zhou et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Evidence for the Role of Active Site Residues in the Hairpin Ribozyme from Molecular Simulations along the Reaction Path

(2014) Hugh Heldenbrand et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Ensemble MD simulations restrained via crystallographic data: Accurate structure leads to accurate dynamics

(2014) Yi Xue et al.   PROTEIN SCIENCE

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

(2014) Antonija Kuzmanic et al.   Nature Communications

The active site of hen egg-white lysozyme: flexibility and chemical bonding

(2014) Jeanette Held et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Resolution of structural heterogeneity in dynamic crystallography

(2013) Zhong Ren et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

(2013) Daniel R. Roe et al.   Journal of Chemical Theory and Computation

Derivation of Fixed Partial Charges for Amino Acids Accommodating a Specific Water Model and Implicit Polarization

(2013) David S. Cerutti et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Peptide Crystal Simulations Reveal Hidden Dynamics

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

Automated identification of functional dynamic contact networks from X-ray crystallography

(2013) Henry van den Bedem et al.   NATURE METHODS

Protein structural ensembles are revealed by redefining X-ray electron density noise

(2013) P. T. Lang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Towards automated crystallographic structure refinement withphenix.refine

(2012) Pavel V. Afonine et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ1 and χ2 Dihedral Angles

(2012) Robert B. Best et al.   Journal of Chemical Theory and Computation

Modelling dynamics in protein crystal structures by ensemble refinement

(2012) B Tom Burnley et al.   eLife

Overview of theCCP4 suite and current developments

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

All-atom modeling of anisotropic atomic fluctuations in protein crystal structures

(2011) Jeffrey Hafner et al.   JOURNAL OF CHEMICAL PHYSICS

Mining electron density for functionally relevant protein polysterism in crystal structures

(2010) James S. Fraser et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

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

Automated electron-density sampling reveals widespread conformational polymorphism in proteins

(2010) P. Therese Lang et al.   PROTEIN SCIENCE

Evidence of Functional Protein Dynamics from X-Ray Crystallographic Ensembles

(2010) Jonathan E. Kohn et al.   PLoS Computational Biology

Modeling discrete heterogeneity in X-ray diffraction data by fitting multi-conformers

(2009) Henry van den Bedem et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Application of Elastic Network Models to Proteins in the Crystalline State

(2009) Demian Riccardi 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

Protein allostery, signal transmission and dynamics: a classification scheme of allosteric mechanisms

(2009) Chung-Jung Tsai et al.   Molecular BioSystems

Simulations of a Protein Crystal: Explicit Treatment of Crystallization Conditions Links Theory and Experiment in the Streptavidin−Biotin Complex†

(2008) David S. Cerutti et al.   BIOCHEMISTRY

Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations

(2008) In Suk Joung et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Molecular Dynamics Simulations for Water and Ions in Protein Crystals

(2008) Zhongqiao Hu et al.   LANGMUIR

Comparisons of experimental and computed protein anisotropic temperature factors

(2008) Lei Yang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS