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

Elucidating Molecular Motion through Structural and Dynamic Filters of Energy-Minimized Conformer Ensembles

(2014) Prashant S. Emani et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Statistical Mechanics of the Denatured State of a Protein Using Replica-Averaged Metadynamics

(2014) Carlo Camilloni et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The ensemble nature of allostery

(2014) Hesam N. Motlagh et al.   NATURE

Structure determination of noncanonical RNA motifs guided by 1H NMR chemical shifts

(2014) Parin Sripakdeevong et al.   NATURE METHODS

Measuring similarity between dynamic ensembles of biomolecules

(2014) Shan Yang et al.   NATURE METHODS

Determination of damage-free crystal structure of an X-ray–sensitive protein using an XFEL

(2014) Kunio Hirata et al.   NATURE METHODS

Characterizing RNA ensembles from NMR data with kinematic models

(2014) Rasmus Fonseca et al.   NUCLEIC ACIDS RESEARCH

Searching for missing heritability: Designing rare variant association studies

(2014) O. Zuk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Diffuse X-Ray Scattering to Model Protein Motions

(2014) Michael E. Wall et al.   STRUCTURE

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

(2014) Daniel A. Keedy et al.   STRUCTURE

Optical measurements of long-range protein vibrations

(2014) Gheorghe Acbas et al.   Nature Communications

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

(2014) Antonija Kuzmanic et al.   Nature Communications

Simultaneous use of solution NMR and X-ray data inREFMAC5 for joint refinement/detection of structural differences

(2014) Mauro Rinaldelli et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Mapping the Population of Protein Conformational Energy Sub-States from NMR Dipolar Couplings

(2013) Paul Guerry et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

A Comparative CEST NMR Study of Slow Conformational Dynamics of Small GTPases Complexed with GTP and GTP Analogues

(2013) Dong Long et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Characterization of the Interdomain Motions in Hen Lysozyme Using Residual Dipolar Couplings as Replica-Averaged Structural Restraints in Molecular Dynamics Simulations

(2013) Alfonso De Simone et al.   BIOCHEMISTRY

Internal protein dynamics on ps to μs timescales as studied by multi-frequency 15N solid-state NMR relaxation

(2013) Tatiana Zinkevich et al.   JOURNAL OF BIOMOLECULAR NMR

Amplitudes and time scales of picosecond-to-microsecond motion in proteins studied by solid-state NMR: a critical evaluation of experimental approaches and application to crystalline ubiquitin

(2013) Jens D. Haller et al.   JOURNAL OF BIOMOLECULAR NMR

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

A General Method for Constructing Atomic-Resolution RNA Ensembles using NMR Residual Dipolar Couplings: The Basis for Interhelical Motions Revealed

(2013) Loïc Salmon et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Recovering a Representative Conformational Ensemble from Underdetermined Macromolecular Structural Data

(2013) Konstantin Berlin et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Microscopic Insights into the NMR Relaxation-Based Protein Conformational Entropy Meter

(2013) Vignesh Kasinath 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

Divergent evolution of protein conformational dynamics in dihydrofolate reductase

(2013) Gira Bhabha et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

NMR paves the way for atomic level descriptions of sparsely populated, transiently formed biomolecular conformers

(2013) A. Sekhar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Integrative Structural Biology

(2013) A. B. Ward et al.   SCIENCE

Characterization of disordered proteins with ENSEMBLE

(2012) Mickaël Krzeminski et al.   BIOINFORMATICS

Computational design of a Diels–Alderase from a thermophilic esterase: the importance of dynamics

(2012) Mats Linder et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Site-Resolved Measurement of Microsecond-to-Millisecond Conformational-Exchange Processes in Proteins by Solid-State NMR Spectroscopy

(2012) Martin Tollinger et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The spatial architecture of protein function and adaptation

(2012) Richard N. McLaughlin Jr et al.   NATURE

Protein activity regulation by conformational entropy

(2012) Shiou-Ru Tzeng et al.   NATURE

Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing

(2012) Timothy A Whitehead et al.   NATURE BIOTECHNOLOGY

Spatial elucidation of motion in proteins by ensemble-based structure calculation using exact NOEs

(2012) Beat Vögeli et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Iterative approach to computational enzyme design

(2012) H. K. Privett et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Improving the Accuracy of Macromolecular Structure Refinement at 7 Å Resolution

(2012) Axel T. Brunger et al.   STRUCTURE

Modelling dynamics in protein crystal structures by ensemble refinement

(2012) B Tom Burnley et al.   eLife

Solid-State NMR Measurements of Asymmetric Dipolar Couplings Provide Insight into Protein Side-Chain Motion

(2011) Paul Schanda et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

A Hydrogen Bond Regulates Slow Motions in Ubiquitin by Modulating a β-Turn Flip

(2011) Arshdeep Sidhu et al.   JOURNAL OF MOLECULAR BIOLOGY

Time Scales of Slow Motions in Ubiquitin Explored by Heteronuclear Double Resonance

(2011) Nicola Salvi et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Towards a robust description of intrinsic protein disorder using nuclear magnetic resonance spectroscopy

(2011) Robert Schneider et al.   Molecular BioSystems

Solution structure of a minor and transiently formed state of a T4 lysozyme mutant

(2011) Guillaume Bouvignies et al.   NATURE

Femtosecond X-ray protein nanocrystallography

(2011) Henry N. Chapman et al.   NATURE

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

A Dynamic Knockout Reveals That Conformational Fluctuations Influence the Chemical Step of Enzyme Catalysis

(2011) G. Bhabha et al.   SCIENCE

Computational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin

(2011) S. J. Fleishman et al.   SCIENCE

Comparison of NMR and crystal structures highlights conformational isomerism in protein active sites

(2010) Pedro Serrano et al.   Acta Crystallographica Section F-Structural Biology and Crystallization Communications

Protein Flexibility and Conformational Entropy in Ligand Design Targeting the Carbohydrate Recognition Domain of Galectin-3

(2010) Carl Diehl et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Super-resolution biomolecular crystallography with low-resolution data

(2010) Gunnar F. Schröder et al.   NATURE

The dynameomics rotamer library: Amino acid side chain conformations and dynamics from comprehensive molecular dynamics simulations in water

(2010) Alexander D. Scouras et al.   PROTEIN SCIENCE

Modeling Conformational Ensembles of Slow Functional Motions in Pin1-WW

(2010) Faruck Morcos 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

Protein Sectors: Evolutionary Units of Three-Dimensional Structure

(2009) Najeeb Halabi et al.   CELL

High-resolution protein structure determination starting with a global fold calculated from exact solutions to the RDC equations

(2009) Jianyang Zeng et al.   JOURNAL OF BIOMOLECULAR NMR

Using generalized ensemble simulations and Markov state models to identify conformational states

(2009) Gregory R. Bowman et al.   METHODS

Hidden alternative structures of proline isomerase essential for catalysis

(2009) James S. Fraser et al.   NATURE

Protein Dynamism and Evolvability

(2009) N. Tokuriki et al.   SCIENCE

Using relaxation dispersion NMR spectroscopy to determine structures of excited, invisible protein states

(2008) D. Flemming Hansen et al.   JOURNAL OF BIOMOLECULAR NMR

Microsecond Molecular Dynamics Simulation Shows Effect of Slow Loop Dynamics on Backbone Amide Order Parameters of Proteins†

(2008) Paul Maragakis et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Protein Side-Chain Dynamics As Observed by Solution- and Solid-State NMR Spectroscopy: A Similarity Revealed

(2008) Vipin Agarwal et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Consistent blind protein structure generation from NMR chemical shift data

(2008) Y. Shen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2008) O. F. Lange et al.   SCIENCE