Fine structure of conformational ensembles in adenylate kinase

Constrained Maximum Likelihood Estimation of Relative Abundances of Protein Conformation in a Heterogeneous Mixture From Small Angle X-Ray Scattering Intensity Measurements

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GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

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Global Transitions of Proteins Explored by a Multiscale Hybrid Methodology: Application to Adenylate Kinase

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High-quality protein backbone reconstruction from alpha carbons using Gaussian mixture models

(2013) Benjamin L. Moore et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Molecular Dynamics Studies on the Conformational Transitions of Adenylate Kinase: A Computational Evidence for the Conformational Selection Mechanism

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Exploring the Dynamic Functional Landscape of Adenylate Kinase Modulated by Substrates

(2012) Yong Wang et al.   Journal of Chemical Theory and Computation

Computing Free Energy of a Large-Scale Allosteric Transition in Adenylate Kinase Using All Atom Explicit Solvent Simulations

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Biomolecular dynamics: order–disorder transitions and energy landscapes

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The role of protein conformational fluctuations in allostery, function, and evolution

(2011) James O. Wrabl et al.   BIOPHYSICAL CHEMISTRY

Large-scale motions in the adenylate kinase solution ensemble: Coarse-grained simulations and comparison with solution X-ray scattering

(2011) Michael D. Daily et al.   CHEMICAL PHYSICS

Many Local Motions Cooperate to Produce the Adenylate Kinase Conformational Transition

(2010) Michael D. Daily et al.   JOURNAL OF MOLECULAR BIOLOGY

SMOG@ctbp: simplified deployment of structure-based models in GROMACS

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Accommodation of aminoacyl-tRNA into the ribosome involves reversible excursions along multiple pathways

(2010) P. C. Whitford et al.   RNA

Noncooperative Folding of Subdomains in Adenylate Kinase†

(2009) Louise Rundqvist et al.   BIOCHEMISTRY

Zipping and Unzipping of Adenylate Kinase: Atomistic Insights into the Ensemble of Open↔Closed Transitions

(2009) Oliver Beckstein et al.   JOURNAL OF MOLECULAR BIOLOGY

Rational modulation of conformational fluctuations in adenylate kinase reveals a local unfolding mechanism for allostery and functional adaptation in proteins

(2009) T. P. Schrank et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Improved prediction of protein side-chain conformations with SCWRL4

(2009) Georgii G. Krivov et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Small- and Large-Scale Conformational Changes of Adenylate Kinase: A Molecular Dynamics Study of the Subdomain Motion and Mechanics

(2008) Francesco Pontiggia et al.   BIOPHYSICAL JOURNAL

Single Molecule Conformational Dynamics of Adenylate Kinase:  Energy Landscape, Structural Correlations, and Transition State Ensembles

(2008) Qiang Lu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Src Kinase Conformational Activation: Thermodynamics, Pathways, and Mechanisms

(2008) Sichun Yang et al.   PLoS Computational Biology