Exposing Hidden Alternative Backbone Conformations in X-ray Crystallography Using qFit

Integrative, dynamic structural biology at atomic resolution—it's about time

(2015) Henry van den Bedem et al.   NATURE METHODS

On the relationship between NMR-derived amide order parameters and protein backbone entropy changes

(2015) Kim A. Sharp et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

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

Visualizing a protein quake with time-resolved X-ray scattering at a free-electron laser

(2014) David Arnlund et al.   NATURE METHODS

Characterizing RNA ensembles from NMR data with kinematic models

(2014) Rasmus Fonseca et al.   NUCLEIC ACIDS RESEARCH

Crystal Cryocooling Distorts Conformational Heterogeneity in a Model Michaelis Complex of DHFR

(2014) Daniel A. Keedy et al.   STRUCTURE

Multiscale Conformational Heterogeneity in Staphylococcal Protein A: Possible Determinant of Functional Plasticity

(2014) Lindsay N. Deis et al.   STRUCTURE

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

(2014) Antonija Kuzmanic et al.   Nature Communications

Correlated motions are a fundamental property of β-sheets

(2014) R. Bryn Fenwick et al.   Nature Communications

Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways

(2013) Kai J. Kohlhoff et al.   Nature Chemistry

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

Dead-end elimination with perturbations (DEEPer): A provable protein design algorithm with continuous sidechain and backbone flexibility

(2013) Mark A. Hallen et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The Role of Local Backrub Motions in Evolved and Designed Mutations

(2012) Daniel A. Keedy et al.   PLoS Computational Biology

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

Protein conformational dynamics in the mechanism of HIV-1 protease catalysis

(2011) V. Y. Torbeev et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accessing protein conformational ensembles using room-temperature X-ray crystallography

(2011) J. S. Fraser et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Automated electron-density sampling reveals widespread conformational polymorphism in proteins

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

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

MolProbity: all-atom structure validation for macromolecular crystallography

(2009) Vincent B. Chen et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Hidden alternative structures of proline isomerase essential for catalysis

(2009) James S. Fraser et al.   NATURE

Sending Signals Dynamically

(2009) R. G. Smock et al.   SCIENCE

Algorithm for backrub motions in protein design

(2008) I. Georgiev et al.   BIOINFORMATICS

Efficient Algorithms to Explore Conformation Spaces of Flexible Protein Loops

(2008) P. Yao et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Backrub-Like Backbone Simulation Recapitulates Natural Protein Conformational Variability and Improves Mutant Side-Chain Prediction

(2008) Colin A. Smith et al.   JOURNAL OF MOLECULAR BIOLOGY

Peptide-plane flipping in proteins

(2002) Steven Hayward   PROTEIN SCIENCE