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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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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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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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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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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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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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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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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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Oligomer Formation of Amyloid-β(29–42) from Its Monomers Using the Hamiltonian Replica-Permutation Molecular Dynamics Simulation

The journal of physical chemistry. B, 2016-07, Vol.120 (27), p.6555-6561

2016

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Effects of a Hydrophilic/Hydrophobic Interface on Amyloid‑β Peptides Studied by Molecular Dynamics Simulations and NMR Experiments

The journal of physical chemistry. B, 2019-01, Vol.123 (1), p.160-169

2019

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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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Dimerization Process of Amyloid-β(29–42) Studied by the Hamiltonian Replica-Permutation Molecular Dynamics Simulations

The journal of physical chemistry. B, 2014-10, Vol.118 (39), p.11428-11436

2014

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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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Replica-Permutation Method with the Suwa–Todo Algorithm beyond the Replica-Exchange Method

Journal of chemical theory and computation, 2013-01, Vol.9 (1), p.570-581

2013

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Hamiltonian replica-permutation method and its applications to an alanine dipeptide and amyloid-β(29-42) peptides

Journal of computational chemistry, 2013-11, Vol.34 (29), p.2493-2497

2013

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Key Residue for Aggregation of Amyloid‑β Peptides

ACS chemical neuroscience, 2022-11, Vol.13 (22), p.3139-3151

2022

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In vivo genotoxicity of 1,4-dioxane evaluated by liver and bone marrow micronucleus tests and Pig-a assay in rats

Mutation research, 2019-01, Vol.837, p.8-14

2019

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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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Molecular dynamics simulations of amyloid-β peptides in heterogeneous environments

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

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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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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Dissociation process of polyalanine aggregates by free electron laser irradiation

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

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

Amyloid Fibril Disruption by Ultrasonic Cavitation: Nonequilibrium Molecular Dynamics Simulations

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

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

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

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

Oligomer Formation of Amyloid-β(29–42) from Its Monomers Using the Hamiltonian Replica-Permutation Molecular Dynamics Simulation

Effects of a Hydrophilic/Hydrophobic Interface on Amyloid‑β Peptides Studied by Molecular Dynamics Simulations and NMR Experiments

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

Dimerization Process of Amyloid-β(29–42) Studied by the Hamiltonian Replica-Permutation Molecular Dynamics Simulations

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

Replica-Permutation Method with the Suwa–Todo Algorithm beyond the Replica-Exchange Method

Hamiltonian replica-permutation method and its applications to an alanine dipeptide and amyloid-β(29-42) peptides

Key Residue for Aggregation of Amyloid‑β Peptides

In vivo genotoxicity of 1,4-dioxane evaluated by liver and bone marrow micronucleus tests and Pig-a assay in rats

pH replica-exchange method based on discrete protonation states

Molecular dynamics simulations of amyloid-β peptides in heterogeneous environments

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

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

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