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Dissociation process of polyalanine aggregates by free electron laser irradiation

PloS one, 2023-09, Vol.18 (9), p.e0291093-e0291093

2023

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Amyloid Fibril Disruption by Ultrasonic Cavitation: Nonequilibrium Molecular Dynamics Simulations

Journal of the American Chemical Society, 2014-07, Vol.136 (30), p.10549-10552

2014

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Promotion and Inhibition of Amyloid-β Peptide Aggregation: Molecular Dynamics Studies

International journal of molecular sciences, 2021-02, Vol.22 (4), p.1859

2021

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Molecular Dynamics Simulation Studies on the Aggregation of Amyloid-β Peptides and Their Disaggregation by Ultrasonic Wave and Infrared Laser Irradiation

Molecules (Basel, Switzerland), 2022-04, Vol.27 (8), p.2483

2022

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Role of Water Molecules and Helix Structure Stabilization in the Laser-Induced Disruption of Amyloid Fibrils Observed by Nonequilibrium Molecular Dynamics Simulations

The journal of physical chemistry. B, 2021-05, Vol.125 (19), p.4964-4976

2021

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All-Atom Molecular Dynamics Simulation Methods for the Aggregation of Protein and Peptides: Replica Exchange/Permutation and Nonequilibrium Simulations

Methods in molecular biology (Clifton, N.J.), 2022, Vol.2340, p.197

2022

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Ingenuity in performing replica permutation: How to order the state labels for improving sampling efficiency

Journal of computational chemistry, 2023-02, Vol.44 (4), p.534-545

2023

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State-of-the-Art Molecular Dynamics Simulation Studies of RNA-Dependent RNA Polymerase of SARS-CoV-2

International journal of molecular sciences, 2022-09, Vol.23 (18), p.10358

2022

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Tardigrade Secretory-Abundant Heat-Soluble Protein Varies Entrance Propensity Depending on the Amino-Acid Sequence

The journal of physical chemistry. B, 2022-03, Vol.126 (12), p.2361-2368

2022

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pH replica-exchange method based on discrete protonation states

Proteins, structure, function, and bioinformatics, 2011-12, Vol.79 (12), p.3420-3436

2011

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Structural basis of TRPA1 inhibition by HC-030031 utilizing species-specific differences

Scientific reports, 2016-11, Vol.6 (1), p.37460-37460, Article 37460

2016

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Energetics and kinetics of substrate analog-coupled staphylococcal nuclease folding revealed by a statistical mechanical approach

Proceedings of the National Academy of Sciences - PNAS, 2020-08, Vol.117 (33), p.19953-19962

2020

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Coulomb replica-exchange method: Handling electrostatic attractive and repulsive forces for biomolecules

Journal of computational chemistry, 2013-03, Vol.34 (8), p.622-639

2013

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Critical contributions of pre-S1 shoulder and distal TRP box in DAG-activated TRPC6 channel by PIP2 regulation

Scientific reports, 2022-06, Vol.12 (1), p.10766-10766, Article 10766

2022

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Inhibition of amyloid-β(16–22) aggregation by polyphenols using replica permutation with solute tempering molecular dynamics simulation

Biophysics and Physicobiology, 2023, Vol.20(4), pp.e200045

2023

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Molecular dynamics simulations of amyloid-β peptides in heterogeneous environments

Biophysics and Physicobiology, 2022, Vol.19, pp.e190010

2022

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Dynamic properties of SARS-CoV and SARS-CoV-2 RNA-dependent RNA polymerases studied by molecular dynamics simulations

Chemical physics letters, 2021-09, Vol.778, p.138819-138819, Article 138819

2021

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Molecular dynamics simulations of amyloid- β (16–22) peptide aggregation at air–water interfaces

The Journal of chemical physics, 2020-03, Vol.152 (9), p.095101-095101

2020

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Replica permutation with solute tempering for molecular dynamics simulation and its application to the dimerization of amyloid-β fragments

The Journal of chemical physics, 2022-02, Vol.156 (8), p.084109-084109

2022

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Structural basis for promiscuous action of monoterpenes on TRP channels

Communications biology, 2021-03, Vol.4 (1), p.293-293, Article 293

2021

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Replica-exchange method in van der Waals radius space: Overcoming steric restrictions for biomolecules

The Journal of chemical physics, 2010-04, Vol.132 (13), p.134105-134105-8

2010

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Explicit symplectic integrators of molecular dynamics algorithms for rigid-body molecules in the canonical, isobaric-isothermal, and related ensembles

The Journal of chemical physics, 2007-02, Vol.126 (8), p.084103-084103

2007

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Structural and fluctuational difference between two ends of Aβ amyloid fibril: MD simulations predict only one end has open conformations

Scientific reports, 2016-12, Vol.6 (1), p.38422-38422, Article 38422

2016

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“Bucket brigade” using lysine residues in RNA-dependent RNA polymerase of SARS-CoV-2

Biophysical journal, 2021-09, Vol.120 (17), p.3615-3627

2021

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Dissociation process of polyalanine aggregates by free electron laser irradiation

Amyloid Fibril Disruption by Ultrasonic Cavitation: Nonequilibrium Molecular Dynamics Simulations

Promotion and Inhibition of Amyloid-β Peptide Aggregation: Molecular Dynamics Studies

Molecular Dynamics Simulation Studies on the Aggregation of Amyloid-β Peptides and Their Disaggregation by Ultrasonic Wave and Infrared Laser Irradiation

Role of Water Molecules and Helix Structure Stabilization in the Laser-Induced Disruption of Amyloid Fibrils Observed by Nonequilibrium Molecular Dynamics Simulations

All-Atom Molecular Dynamics Simulation Methods for the Aggregation of Protein and Peptides: Replica Exchange/Permutation and Nonequilibrium Simulations

Ingenuity in performing replica permutation: How to order the state labels for improving sampling efficiency

State-of-the-Art Molecular Dynamics Simulation Studies of RNA-Dependent RNA Polymerase of SARS-CoV-2

Tardigrade Secretory-Abundant Heat-Soluble Protein Varies Entrance Propensity Depending on the Amino-Acid Sequence

pH replica-exchange method based on discrete protonation states

Structural basis of TRPA1 inhibition by HC-030031 utilizing species-specific differences

Energetics and kinetics of substrate analog-coupled staphylococcal nuclease folding revealed by a statistical mechanical approach

Coulomb replica-exchange method: Handling electrostatic attractive and repulsive forces for biomolecules

Critical contributions of pre-S1 shoulder and distal TRP box in DAG-activated TRPC6 channel by PIP2 regulation

Inhibition of amyloid-β(16–22) aggregation by polyphenols using replica permutation with solute tempering molecular dynamics simulation

Molecular dynamics simulations of amyloid-β peptides in heterogeneous environments

Dynamic properties of SARS-CoV and SARS-CoV-2 RNA-dependent RNA polymerases studied by molecular dynamics simulations

Molecular dynamics simulations of amyloid- β (16–22) peptide aggregation at air–water interfaces

Replica permutation with solute tempering for molecular dynamics simulation and its application to the dimerization of amyloid-β fragments

Structural basis for promiscuous action of monoterpenes on TRP channels

Replica-exchange method in van der Waals radius space: Overcoming steric restrictions for biomolecules

Explicit symplectic integrators of molecular dynamics algorithms for rigid-body molecules in the canonical, isobaric-isothermal, and related ensembles

Structural and fluctuational difference between two ends of Aβ amyloid fibril: MD simulations predict only one end has open conformations

“Bucket brigade” using lysine residues in RNA-dependent RNA polymerase of SARS-CoV-2

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