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Generalized Born Implicit Solvent Models for Biomolecules

Annual review of biophysics, 2019-05, Vol.48 (1), p.275-296

2019

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Speed of Conformational Change: Comparing Explicit and Implicit Solvent Molecular Dynamics Simulations

Biophysical journal, 2015-03, Vol.108 (5), p.1153-1164

2015

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Protonation and pK changes in protein–ligand binding

Quarterly reviews of biophysics, 2013-05, Vol.46 (2), p.181-209

2013

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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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Partially Assembled Nucleosome Structures at Atomic Detail

Biophysical journal, 2017-02, Vol.112 (3), p.460-472

2017

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The probability of chromatin to be at the nuclear lamina has no systematic effect on its transcription level in fruit flies

Epigenetics & chromatin, 2024-05, Vol.17 (1), p.13-13, Article 13

2024

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The Role of Correlation and Solvation in Ion Interactions with B-DNA

Biophysical journal, 2016-01, Vol.110 (2), p.315-326

2016

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H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations

Nucleic acids research, 2012-07, Vol.40 (Web Server issue), p.W537-W541

2012

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Strong interactions between highly dynamic lamina-associated domains and the nuclear envelope stabilize the 3D architecture of Drosophila interphase chromatin

Epigenetics & chromatin, 2023-05, Vol.16 (1), p.21-25

2023

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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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Charge State of the Globular Histone Core Controls Stability of the Nucleosome

Biophysical journal, 2010-09, Vol.99 (5), p.1577-1585

2010

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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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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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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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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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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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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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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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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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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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Spermine Condenses DNA, but Not RNA Duplexes

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

2017

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Generalized Born Implicit Solvent Models for Biomolecules

Speed of Conformational Change: Comparing Explicit and Implicit Solvent Molecular Dynamics Simulations

Protonation and pK changes in protein–ligand binding

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

Partially Assembled Nucleosome Structures at Atomic Detail

The probability of chromatin to be at the nuclear lamina has no systematic effect on its transcription level in fruit flies

The Role of Correlation and Solvation in Ion Interactions with B-DNA

H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations

Strong interactions between highly dynamic lamina-associated domains and the nuclear envelope stabilize the 3D architecture of Drosophila interphase chromatin

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

Charge State of the Globular Histone Core Controls Stability of the Nucleosome

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

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

Fast Polarizable Water Model for Atomistic Simulations

Two-phase stretching of molecular chains

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

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

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

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

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

Spermine Condenses DNA, but Not RNA Duplexes

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