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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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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.2036-2046

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.11459-11475

2021

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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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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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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 Edition, 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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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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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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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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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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Modeling and Simulation of Ion Channels

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

2012

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

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

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

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

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

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

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

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

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

Modeling and Simulation of Ion Channels

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

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