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Accuracy limit of rigid 3-point water models

The Journal of chemical physics, 2016-08, Vol.145 (7), p.074501-074501

2016

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Building Water Models: A Different Approach

The journal of physical chemistry letters, 2014-11, Vol.5 (21), p.3863-3871

2014

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General Purpose Water Model Can Improve Atomistic Simulations of Intrinsically Disordered Proteins

Journal of chemical theory and computation, 2019-04, Vol.15 (4), p.2620-2634

2019

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Exploring optimization strategies for improving explicit water models: Rigid n-point model and polarizable model based on Drude oscillator

PloS one, 2019-11, Vol.14 (11), p.e0224991-e0224991

2019

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Opposing Effects of Multivalent Ions on the Flexibility of DNA and RNA

Physical review letters, 2016-07, Vol.117 (2), p.028101-028101, Article 028101

2016

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Point charges optimally placed to represent the multipole expansion of charge distributions

PloS one, 2013-07, Vol.8 (7), p.e67715-e67715

2013

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Investigation of the chromosome regions with significant affinity for the nuclear envelope in fruit fly--a model based approach

PloS one, 2014-03, Vol.9 (3), p.e91943-e91943

2014

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Reducing the Secondary Structure Bias in the Generalized Born Model via R6 Effective Radii

Journal of chemical theory and computation, 2010-12, Vol.6 (12), p.3613-3630

2010

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Why Computed Protein Folding Landscapes Are Sensitive to the Water Model

Journal of chemical theory and computation, 2019-01, Vol.15 (1), p.625-636

2019

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Strongly Bent Double-Stranded DNA: Reconciling Theory and Experiment

Frontiers in physics, 2019-11, Vol.7

2019

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Fast Polarizable Water Model for Atomistic Simulations

Journal of chemical theory and computation, 2022-10, Vol.18 (10), p.6324-6333

2022

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Implicit Solvent with Explicit Ions Generalized Born Model in Molecular Dynamics: Application to DNA

Journal of chemical theory and computation, 2024-10, Vol.20 (19), p.8724-8739

2024

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Stretching of Long Double-Stranded DNA and RNA Described by the Same Approach

Journal of chemical theory and computation, 2022-06, Vol.18 (6), p.3911-3920

2022

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Implicit Solvent Model for Million-Atom Atomistic Simulations: Insights into the Organization of 30-nm Chromatin Fiber

Journal of chemical theory and computation, 2016-12, Vol.12 (12), p.5946-5959

2016

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Similarities and Differences between Na+ and K+ Distributions around DNA Obtained with Three Popular Water Models

Journal of chemical theory and computation, 2021-11, Vol.17 (11), p.7246-7259

2021

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High-temperature dynamic behavior in bulk liquid water： A molecular dynamics simulation study using the OPC and TIP4P-Ew potentials

Frontiers of physics, 2018-02, Vol.13 (1), p.25-39, Article 138203

2018

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Protein–Ligand Electrostatic Binding Free Energies from Explicit and Implicit Solvation

Journal of chemical theory and computation, 2015-09, Vol.11 (9), p.4450-4459

2015

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Multidimensional Global Optimization and Robustness Analysis in the Context of Protein–Ligand Binding

Journal of chemical theory and computation, 2020-07, Vol.16 (7), p.4669-4684

2020

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Why Na+ has higher propensity than K+ to condense DNA in a crowded environment

The Journal of chemical physics, 2023-10, Vol.159 (14)

2023

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Accuracy Comparison of Generalized Born Models in the Calculation of Electrostatic Binding Free Energies

Journal of chemical theory and computation, 2018-03, Vol.14 (3), p.1656-1670

2018

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Improving the Accuracy of Physics-Based Hydration-Free Energy Predictions by Machine Learning the Remaining Error Relative to the Experiment

Journal of chemical theory and computation, 2024-01, Vol.20 (1), p.396-410

2024

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Explicit ions/implicit water generalized Born model for nucleic acids

The Journal of chemical physics, 2018-05, Vol.148 (19), p.195101-195101

2018

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Efficient Computation of the Total Solvation Energy of Small Molecules via the R6 Generalized Born Model

Journal of chemical theory and computation, 2012-07, Vol.8 (7), p.2404-2411

2012

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A strategy for reducing gross errors in the generalized Born models of implicit solvation

The Journal of chemical physics, 2011-04, Vol.134 (16), p.164104-164104-15

2011

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Introducing Charge Hydration Asymmetry into the Generalized Born Model

Journal of chemical theory and computation, 2014-04, Vol.10 (4), p.1788-1794

2014

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Accuracy limit of rigid 3-point water models

Building Water Models: A Different Approach

General Purpose Water Model Can Improve Atomistic Simulations of Intrinsically Disordered Proteins

Exploring optimization strategies for improving explicit water models: Rigid n-point model and polarizable model based on Drude oscillator

Opposing Effects of Multivalent Ions on the Flexibility of DNA and RNA

Point charges optimally placed to represent the multipole expansion of charge distributions

Investigation of the chromosome regions with significant affinity for the nuclear envelope in fruit fly--a model based approach

Reducing the Secondary Structure Bias in the Generalized Born Model via R6 Effective Radii

Why Computed Protein Folding Landscapes Are Sensitive to the Water Model

Strongly Bent Double-Stranded DNA: Reconciling Theory and Experiment

Fast Polarizable Water Model for Atomistic Simulations

Implicit Solvent with Explicit Ions Generalized Born Model in Molecular Dynamics: Application to DNA

Stretching of Long Double-Stranded DNA and RNA Described by the Same Approach

Implicit Solvent Model for Million-Atom Atomistic Simulations: Insights into the Organization of 30-nm Chromatin Fiber

Similarities and Differences between Na+ and K+ Distributions around DNA Obtained with Three Popular Water Models

High-temperature dynamic behavior in bulk liquid water： A molecular dynamics simulation study using the OPC and TIP4P-Ew potentials

Protein–Ligand Electrostatic Binding Free Energies from Explicit and Implicit Solvation

Multidimensional Global Optimization and Robustness Analysis in the Context of Protein–Ligand Binding

Why Na+ has higher propensity than K+ to condense DNA in a crowded environment

Accuracy Comparison of Generalized Born Models in the Calculation of Electrostatic Binding Free Energies

Improving the Accuracy of Physics-Based Hydration-Free Energy Predictions by Machine Learning the Remaining Error Relative to the Experiment

Explicit ions/implicit water generalized Born model for nucleic acids

Efficient Computation of the Total Solvation Energy of Small Molecules via the R6 Generalized Born Model

A strategy for reducing gross errors in the generalized Born models of implicit solvation

Introducing Charge Hydration Asymmetry into the Generalized Born Model

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