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Atomic level computational identification of ligand migration pathways between solvent and binding site in myoglobin

Proceedings of the National Academy of Sciences - PNAS, 2008-07, Vol.105 (27), p.9204-9209

2008

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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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Correction to “Fast Polarizable Water Model for Atomistic Simulations”

Journal of chemical theory and computation, 2023-01, Vol.19 (1), p.377-377

2023

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Two-phase stretching of molecular chains

Proceedings of the National Academy of Sciences - PNAS, 2013-02, Vol.110 (8), p.2816-2821

2013

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Bounds on Absolute Gypsy Moth (Lymantria dispar dispar) (Lepidoptera: Erebidae) Population Density as Derived from Counts in Single Milk Carton Traps

Insects (Basel, Switzerland), 2020-10, Vol.11 (10), p.673

2020

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Significant compaction of H4 histone tail upon charge neutralization by acetylation and its mimics, possible effects on chromatin structure

Journal of molecular biology, 2021-03, Vol.433 (6), p.166683-166683, Article 166683

2021

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Three-dimensional Organization of Polytene Chromosomes in Somatic and Germline Tissues of Malaria Mosquitoes

Cells (Basel, Switzerland), 2020-02, Vol.9 (2), p.339

2020

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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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Inclusion of Water Multipoles into the Implicit Solvation Framework Leads to Accuracy Gains

The journal of physical chemistry. B, 2024-06, Vol.128 (24), p.5855-5873

2024

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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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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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Grid-Based Surface Generalized Born Model for Calculation of Electrostatic Binding Free Energies

Journal of chemical information and modeling, 2017-10, Vol.57 (10), p.2505-2513

2017

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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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AmberTools

Journal of chemical information and modeling, 2023-10, Vol.63 (20), p.6183-6191

2023

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Location of a topologically associating domain at the nuclear periphery has no systematic causal effect on its genes transcription levels in drosophila nuclei

Biophysical journal, 2023-02, Vol.122 (3), p.69a-69a

2023

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Spermine Condenses DNA, but Not RNA Duplexes

Biophysical journal, 2017-01, Vol.112 (1), p.22-30

2017

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Charge Hydration Asymmetry: The Basic Principle and How to Use It to Test and Improve Water Models

The journal of physical chemistry. B, 2012-08, Vol.116 (32), p.9776-9783

2012

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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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Why double-stranded RNA resists condensation

Nucleic acids research, 2014-09, Vol.42 (16), p.10823

2014

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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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Atomic level computational identification of ligand migration pathways between solvent and binding site in myoglobin

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

Correction to “Fast Polarizable Water Model for Atomistic Simulations”

Two-phase stretching of molecular chains

Bounds on Absolute Gypsy Moth (Lymantria dispar dispar) (Lepidoptera: Erebidae) Population Density as Derived from Counts in Single Milk Carton Traps

Significant compaction of H4 histone tail upon charge neutralization by acetylation and its mimics, possible effects on chromatin structure

Three-dimensional Organization of Polytene Chromosomes in Somatic and Germline Tissues of Malaria Mosquitoes

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

Inclusion of Water Multipoles into the Implicit Solvation Framework Leads to Accuracy Gains

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

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

Grid-Based Surface Generalized Born Model for Calculation of Electrostatic Binding Free Energies

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

AmberTools

Location of a topologically associating domain at the nuclear periphery has no systematic causal effect on its genes transcription levels in drosophila nuclei

Spermine Condenses DNA, but Not RNA Duplexes

Charge Hydration Asymmetry: The Basic Principle and How to Use It to Test and Improve Water Models

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

Why double-stranded RNA resists condensation

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

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