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On the stability of protein–DNA complexes in molecular dynamics simulations using the CUFIX corrections

Journal of the Korean Physical Society, 2021, 78(5), , pp.461-466

Yoo, Jejoong

2021

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In situ structure and dynamics of DNA origami determined through molecular dynamics simulations

Proceedings of the National Academy of Sciences - PNAS, 2013-12, Vol.110 (50), p.20099-20104

2013

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Conformational changes in the human Cx43/GJA1 gap junction channel visualized using cryo-EM

Nature communications, 2023-02, Vol.14 (1), p.931-931, Article 931

2023

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Single-molecule fingerprinting of protein-drug interaction using a funneled biological nanopore

Nature communications, 2023-04, Vol.14 (1), p.1461-1461, Article 1461

2023

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Improved Parametrization of Li+, Na+, K+, and Mg2+ Ions for All-Atom Molecular Dynamics Simulations of Nucleic Acid Systems

The journal of physical chemistry letters, 2012-01, Vol.3 (1), p.45-50

2012

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Molecular mechanics of DNA bricks: in situ structure, mechanical properties and ionic conductivity

New journal of physics, 2016-05, Vol.18 (5), p.55012

2016

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Effect of DNA Flexibility on Complex Formation of a Cationic Nanoparticle with Double-Stranded DNA

ACS omega, 2021-07, Vol.6 (29), p.18728-18736

2021

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Competitive Binding of Cations to Duplex DNA Revealed through Molecular Dynamics Simulations

The journal of physical chemistry. B, 2012-11, Vol.116 (43), p.12946-12954

2012

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Molecular dynamics simulations of DNA–DNA and DNA–protein interactions

Current opinion in structural biology, 2020-10, Vol.64, p.88-96

2020

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Refined Parameterization of Nonbonded Interactions Improves Conformational Sampling and Kinetics of Protein Folding Simulations

The journal of physical chemistry letters, 2016-10, Vol.7 (19), p.3812-3818

2016

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De novo reconstruction of DNA origami structures through atomistic molecular dynamics simulation

Nucleic acids research, 2016-04, Vol.44 (7), p.3013-3019

2016

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Molecular Dynamics Simulations using Accurate Charge-Charge Interactions Predict Unexpected Phase Behaviors of DNA Controlled by Epigenetic Modifications

Biophysical journal, 2019-02, Vol.116 (3), p.437a-437a

2019

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Water Mediates Recognition of DNA Sequence via Ionic Current Blockade in a Biological Nanopore

ACS nano, 2016-04, Vol.10 (4), p.4644-4651

2016

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New tricks for old dogs: improving the accuracy of biomolecular force fields by pair-specific corrections to non-bonded interactionsElectronic supplementary information (ESI) available. See DOI: 10.1039/c7cp08185e

2018-03

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Sliding, Fast and Slow: Distinct Diffusion Mechanisms of Eukaryotic and Prokaryotic DNA Clamps

Biophysical journal, 2020-02, Vol.118 (3), p.71a-71a

2020

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Improved model of hydrated calcium ion for molecular dynamics simulations using classical biomolecular force fields

Biopolymers, 2016-10, Vol.105 (10), p.752-763

2016

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Three-Dimensional Stress Field around a Membrane Protein: Atomistic and Coarse-Grained Simulation Analysis of Gramicidin A

Biophysical journal, 2013-01, Vol.104 (1), p.117-127

2013

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Improved Parameterization of Amine-Carboxyate, Amine-Phosphate, and Aliphatic Carbon-Carbon Interactions for Molecular Dynamics Simulations using the Charmm and Amber Force Fields

Biophysical journal, 2016-02, Vol.110 (3), p.646a-646a

2016

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Large-Conductance Transmembrane Porin Made from DNA Origami

ACS nano, 2016-09, Vol.10 (9), p.8207-8214

2016

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The Physics of DNA in Confinement

Biophysical journal, 2014-01, Vol.106 (2), p.76a-76a

2014

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In Situ Structure and Dynamics of DNA Origami Determined Through Molecular Dynamics Simulations

Biophysical journal, 2014-01, Vol.106 (2), p.695a-695a

2014

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Web-based applications for automated generation of functionalized graphene and carbon nanotube for molecular dynamics simulations and automated three-dimensional analysis of ion flow through nanopores

Current applied physics, 2024-11, Vol.67, p.30-37

2024

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GPU acceleration of many‐body perturbation theory methods in MOLGW with OpenACC

International journal of quantum chemistry, 2024-03, Vol.124 (5), p.n/a

2024

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Correction: Aggregation or phase separation can be induced in highly charged proteins by small charged biomolecules

Soft matter, 2023-01, Vol.19 (3), p.574-574

2023

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Sequence-dependent twist-bend coupling in DNA minicircles

Nanoscale, 2021-12, Vol.13 (47), p.2186-2196

2021

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On the stability of protein–DNA complexes in molecular dynamics simulations using the CUFIX corrections

In situ structure and dynamics of DNA origami determined through molecular dynamics simulations

Conformational changes in the human Cx43/GJA1 gap junction channel visualized using cryo-EM

Single-molecule fingerprinting of protein-drug interaction using a funneled biological nanopore

Improved Parametrization of Li+, Na+, K+, and Mg2+ Ions for All-Atom Molecular Dynamics Simulations of Nucleic Acid Systems

Molecular mechanics of DNA bricks: in situ structure, mechanical properties and ionic conductivity

Effect of DNA Flexibility on Complex Formation of a Cationic Nanoparticle with Double-Stranded DNA

Competitive Binding of Cations to Duplex DNA Revealed through Molecular Dynamics Simulations

Molecular dynamics simulations of DNA–DNA and DNA–protein interactions

Refined Parameterization of Nonbonded Interactions Improves Conformational Sampling and Kinetics of Protein Folding Simulations

De novo reconstruction of DNA origami structures through atomistic molecular dynamics simulation

Molecular Dynamics Simulations using Accurate Charge-Charge Interactions Predict Unexpected Phase Behaviors of DNA Controlled by Epigenetic Modifications

Water Mediates Recognition of DNA Sequence via Ionic Current Blockade in a Biological Nanopore

New tricks for old dogs: improving the accuracy of biomolecular force fields by pair-specific corrections to non-bonded interactionsElectronic supplementary information (ESI) available. See DOI: 10.1039/c7cp08185e

Sliding, Fast and Slow: Distinct Diffusion Mechanisms of Eukaryotic and Prokaryotic DNA Clamps

Improved model of hydrated calcium ion for molecular dynamics simulations using classical biomolecular force fields

Three-Dimensional Stress Field around a Membrane Protein: Atomistic and Coarse-Grained Simulation Analysis of Gramicidin A

Improved Parameterization of Amine-Carboxyate, Amine-Phosphate, and Aliphatic Carbon-Carbon Interactions for Molecular Dynamics Simulations using the Charmm and Amber Force Fields

Large-Conductance Transmembrane Porin Made from DNA Origami

The Physics of DNA in Confinement

In Situ Structure and Dynamics of DNA Origami Determined Through Molecular Dynamics Simulations

Web-based applications for automated generation of functionalized graphene and carbon nanotube for molecular dynamics simulations and automated three-dimensional analysis of ion flow through nanopores

GPU acceleration of many‐body perturbation theory methods in MOLGW with OpenACC

Correction: Aggregation or phase separation can be induced in highly charged proteins by small charged biomolecules

Sequence-dependent twist-bend coupling in DNA minicircles

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