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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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Cryo-EM structures of human Cx36/GJD2 neuronal gap junction channel

Nature communications, 2023-03, Vol.14 (1), p.1347-1347, Article 1347

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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Molecular Dynamics of Membrane-Spanning DNA Channels: Conductance Mechanism, Electro-Osmotic Transport, and Mechanical Gating

The journal of physical chemistry letters, 2015-12, Vol.6 (23), p.4680-4687

2015

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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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Cryo-EM structure of human Cx31.3/GJC3 connexin hemichannel

Science advances, 2020-08, Vol.6 (35), p.eaba4996-eaba4996

2020

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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, 2021-03, p.461-466

Yoo Jejoong

2021

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

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

2016

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Modeling and Simulation of Ion Channels

Chemical reviews, 2012-12, Vol.112 (12), p.6250-6284

2012

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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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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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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 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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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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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

Cryo-EM structures of human Cx36/GJD2 neuronal gap junction channel

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

Molecular Dynamics of Membrane-Spanning DNA Channels: Conductance Mechanism, Electro-Osmotic Transport, and Mechanical Gating

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

Cryo-EM structure of human Cx31.3/GJC3 connexin hemichannel

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

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

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

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

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

Modeling and Simulation of Ion Channels

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

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

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

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

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

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