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New tricks for old dogs: improving the accuracy of biomolecular force fields by pair-specific corrections to non-bonded interactions

Physical chemistry chemical physics : PCCP, 2018, Vol.20 (13), p.8432-8449

2018

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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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Improved Parameterization of Amine–Carboxylate and Amine–Phosphate Interactions for Molecular Dynamics Simulations Using the CHARMM and AMBER Force Fields

Journal of chemical theory and computation, 2016-01, Vol.12 (1), p.430-443

2016

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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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The structure and intermolecular forces of DNA condensates

Nucleic acids research, 2016-03, Vol.44 (5), p.2036

2016

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Direct evidence for sequence-dependent attraction between double-stranded DNA controlled by methylation

Nature communications, 2016-03, Vol.7 (1), p.11045-11045, Article 11045

2016

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Effects of cytosine modifications on DNA flexibility and nucleosome mechanical stability

Nature communications, 2016-02, Vol.7 (1), p.10813-10813, Article 10813

2016

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DNA sequence and methylation prescribe the inside-out conformational dynamics and bending energetics of DNA minicircles

Nucleic acids research, 2021-11, Vol.49 (20), p.11459

2021

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Membrane-Mediated Protein-Protein Interactions and Connection to Elastic Models: A Coarse-Grained Simulation Analysis of Gramicidin A Association

Biophysical journal, 2013-01, Vol.104 (1), p.128-138

2013

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Does Arginine Remain Protonated in the Lipid Membrane? Insights from Microscopic pKa Calculations

Biophysical journal, 2008-04, Vol.94 (8), p.L61-L63

2008

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Improved Parameterization of Protein–DNA Interactions for Molecular Dynamics Simulations of PCNA Diffusion on DNA

Journal of chemical theory and computation, 2020-07, Vol.16 (7), p.4006-4013

2020

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Curvature Generation and Pressure Profile Modulation in Membrane by Lysolipids: Insights from Coarse-Grained Simulations

Biophysical journal, 2009-10, Vol.97 (8), p.2267-2276

2009

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Rational Design and Construction of Hierarchical Superstructures Using Shape-Persistent Organic Cages: Porphyrin Box-Based Metallosupramolecular Assemblies

Journal of the American Chemical Society, 2018-11, Vol.140 (44), p.14547-14551

2018

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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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Mono‐allyloxylated Cucurbit[7]uril Acts as an Unconventional Amphiphile To Form Light‐Responsive Vesicles

Angewandte Chemie (International ed.), 2018-03, Vol.57 (12), p.3132-3136

International ed. in English, 2018

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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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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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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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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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New tricks for old dogs: improving the accuracy of biomolecular force fields by pair-specific corrections to non-bonded interactions

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

Improved Parameterization of Amine–Carboxylate and Amine–Phosphate Interactions for Molecular Dynamics Simulations Using the CHARMM and AMBER Force Fields

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

The structure and intermolecular forces of DNA condensates

Direct evidence for sequence-dependent attraction between double-stranded DNA controlled by methylation

Effects of cytosine modifications on DNA flexibility and nucleosome mechanical stability

DNA sequence and methylation prescribe the inside-out conformational dynamics and bending energetics of DNA minicircles

Membrane-Mediated Protein-Protein Interactions and Connection to Elastic Models: A Coarse-Grained Simulation Analysis of Gramicidin A Association

Does Arginine Remain Protonated in the Lipid Membrane? Insights from Microscopic pKa Calculations

Improved Parameterization of Protein–DNA Interactions for Molecular Dynamics Simulations of PCNA Diffusion on DNA

Curvature Generation and Pressure Profile Modulation in Membrane by Lysolipids: Insights from Coarse-Grained Simulations

Rational Design and Construction of Hierarchical Superstructures Using Shape-Persistent Organic Cages: Porphyrin Box-Based Metallosupramolecular Assemblies

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

Mono‐allyloxylated Cucurbit[7]uril Acts as an Unconventional Amphiphile To Form Light‐Responsive Vesicles

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

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

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

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

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