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Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation
Gaussian accelerated molecular dynamics (GaMD) approach for simultaneous enhanced sampling and free energy calculation of biomolecules is presented. Expand
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Activation and dynamic network of the M2 muscarinic receptor
G-protein-coupled receptors (GPCRs) mediate cellular responses to various hormones and neurotransmitters and are important targets for treating a wide spectrum of diseases. Although significantExpand
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Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation
We systematically compare the accuracy of different reweighting algorithms including the exponential average, Maclaurin series, and cumulant expansion on three model systems: alanine dipeptide, chignolin, and Trp-cage. Expand
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Allosteric effects of sodium ion binding on activation of the m3 muscarinic g-protein-coupled receptor.
G-protein-coupled receptors (GPCRs) are important membrane proteins that mediate cellular signaling and represent primary targets for about one-third of currently marketed drugs. Recent x-rayExpand
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Striking Plasticity of CRISPR-Cas9 and Key Role of Non-target DNA, as Revealed by Molecular Simulations
The CRISPR (clustered regularly interspaced short palindromic repeats)-Cas9 system recently emerged as a transformative genome-editing technology that is innovating basic bioscience and appliedExpand
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Population Based Reweighting of Scaled Molecular Dynamics
Molecular dynamics simulation using enhanced sampling methods is one of the powerful computational tools used to explore protein conformations and free energy landscapes. Enhanced sampling methodsExpand
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CRISPR-Cas9 conformational activation as elucidated from enhanced molecular simulations
Significance The CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats–CRISPR-associated protein 9) system recently emerged as a transformative genome editing technology that isExpand
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G-protein coupled receptors: advances in simulation and drug discovery.
G-protein coupled receptors (GPCRs), the largest family of human membrane proteins, mediate cellular signaling and represent primary targets of about one third of currently marketed drugs. GPCRsExpand
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All-atom multiscaling and new ensembles for dynamical nanoparticles.
Viruses and other nanoparticles have mixed microscopic/macroscopic character. Thus it is natural to develop an understanding of their dynamics via a multiscale analysis of the Liouville equationExpand
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Accelerated Molecular Dynamics Simulations of Protein Folding
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