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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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The nucleosome: from structure to function through physics

Current opinion in structural biology, 2019-06, Vol.56, p.119-130

2019

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Water models for biomolecular simulations

Wiley interdisciplinary reviews. Computational molecular science, 2018-03, Vol.8 (2), p.e1347-n/a

2018

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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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Biologically relevant small variations of intra-cellular pH can have significant effect on stability of protein-DNA complexes, including the nucleosome

Frontiers in molecular biosciences, 2023-04, Vol.10, p.1067787-1067787

Onufriev, Alexey V

2023

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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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Modulation of nucleosomal DNA accessibility via charge-altering post-translational modifications in histone core

Epigenetics & chromatin, 2018-03, Vol.11 (1), p.11-11, Article 11

2018

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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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Linear relationship between peak and season-long abundances in insects

PloS one, 2018-02, Vol.13 (2), p.e0193110-e0193110

2018

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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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How to Count Bugs: A Method to Estimate the Most Probable Absolute Population Density and Its Statistical Bounds from a Single Trap Catch

Insects (Basel, Switzerland), 2021-10, Vol.12 (10), p.932

2021

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Melting Points of OPC and OPC3 Water Models

ACS omega, 2020-10, Vol.5 (39), p.25087-25094

2020

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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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Chromosome-nuclear envelope attachments affect interphase chromosome territories and entanglement

Epigenetics & chromatin, 2018-01, Vol.11 (1), p.3-3, Article 3

2018

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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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Strongly Bent Double-Stranded DNA: Reconciling Theory and Experiment

Frontiers in physics, 2019-11, Vol.7

2019

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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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Generalized Born Implicit Solvent Models for Biomolecules

The nucleosome: from structure to function through physics

Water models for biomolecular simulations

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

Biologically relevant small variations of intra-cellular pH can have significant effect on stability of protein-DNA complexes, including the nucleosome

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

Modulation of nucleosomal DNA accessibility via charge-altering post-translational modifications in histone core

Partially Assembled Nucleosome Structures at Atomic Detail

Linear relationship between peak and season-long abundances in insects

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

How to Count Bugs: A Method to Estimate the Most Probable Absolute Population Density and Its Statistical Bounds from a Single Trap Catch

Melting Points of OPC and OPC3 Water Models

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

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

Chromosome-nuclear envelope attachments affect interphase chromosome territories and entanglement

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

Strongly Bent Double-Stranded DNA: Reconciling Theory and Experiment

Correction to “Fast Polarizable Water Model for Atomistic Simulations”

Two-phase stretching of molecular chains

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