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Assessing the Current State of Amber Force Field Modifications for DNA

Journal of chemical theory and computation, 2016-08, Vol.12 (8), p.4114-4127

2016

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Refinement of the Sugar–Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B‑DNA

Journal of chemical theory and computation, 2015-12, Vol.11 (12), p.5723-5736

2015

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Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions

Journal of chemical theory and computation, 2019-05, Vol.15 (5), p.3288-3305

2019

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Effect of Monovalent Ion Parameters on Molecular Dynamics Simulations of G‑Quadruplexes

Journal of chemical theory and computation, 2017-08, Vol.13 (8), p.3911-3926

2017

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QM/MM Calculations on Protein–RNA Complexes: Understanding Limitations of Classical MD Simulations and Search for Reliable Cost-Effective QM Methods

Journal of chemical theory and computation, 2018-10, Vol.14 (10), p.5419-5433

2018

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Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies

Journal of chemical theory and computation, 2016-09, Vol.12 (9), p.4534-4548

2016

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Coarse-Grained Simulations Complemented by Atomistic Molecular Dynamics Provide New Insights into Folding and Unfolding of Human Telomeric G‑Quadruplexes

Journal of chemical theory and computation, 2016-12, Vol.12 (12), p.6077-6097

2016

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A- to B‑DNA Transition in AMBER Force Fields and Its Coupling to Sugar Pucker

Journal of chemical theory and computation, 2018-01, Vol.14 (1), p.319-328

2018

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RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview

Chemical reviews, 2018-04, Vol.118 (8), p.4177-4338

2018

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Role of Fine Structural Dynamics in Recognition of Histone H3 by HP1γ(CSD) Dimer and Ability of Force Fields to Describe Their Interaction Network

Journal of chemical theory and computation, 2019-10, Vol.15 (10), p.5659-5673

2019

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Fine-Tuning of the AMBER RNA Force Field with a New Term Adjusting Interactions of Terminal Nucleotides

Journal of chemical theory and computation, 2020-06, Vol.16 (6), p.3936-3946

2020

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Insights into Stability and Folding of GNRA and UNCG Tetraloops Revealed by Microsecond Molecular Dynamics and Well-Tempered Metadynamics

Journal of chemical theory and computation, 2015-08, Vol.11 (8), p.3866-3877

2015

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Stability of Two-Quartet G-Quadruplexes and Their Dimers in Atomistic Simulations

Journal of chemical theory and computation, 2020-06, Vol.16 (6), p.3447-3463

2020

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Simulations of A‑RNA Duplexes. The Effect of Sequence, Solute Force Field, Water Model, and Salt Concentration

The journal of physical chemistry. B, 2012-08, Vol.116 (33), p.9899-9916

2012

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Sequential electron transfer governs the UV-induced self-repair of DNA photolesions

Chemical science (Cambridge), 2018-03, Vol.9 (12), p.3131-3140

2018

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Reactive Conformation of the Active Site in the Hairpin Ribozyme Achieved by Molecular Dynamics Simulations with ε/ζ Force Field Reparametrizations

The journal of physical chemistry. B, 2015-03, Vol.119 (11), p.4220-4229

2015

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UV-induced hydrogen transfer in DNA base pairs promoted by dark nπ states

Chemical communications (Cambridge, England), 2020-01, Vol.56 (2), p.21-24

2020

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rRNA C‑Loops: Mechanical Properties of a Recurrent Structural Motif

Journal of chemical theory and computation, 2017-07, Vol.13 (7), p.3359-3371

2017

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How to understand quantum chemical computations on DNA and RNA systems? A practical guide for non-specialists

Methods (San Diego, Calif.), 2013-11, Vol.64 (1), p.3-11

2013

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Solvent effects on the photochemistry of 4-aminoimidazole-5-carbonitrile, a prebiotically plausible precursor of purines

Physical chemistry chemical physics : PCCP, 2014-09, Vol.16 (33), p.17617-17626

2014

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Molecular dynamics simulations of sarcin-ricin rRNA motif

Nucleic acids research, 2006-01, Vol.34 (2), p.697-708

2006

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Electron-driven proton transfer enables nonradiative photodeactivation in microhydrated 2-aminoimidazole

Faraday discussions, 2018-12, Vol.212, p.345-358

2018

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Elastic properties of ribosomal RNA building blocks: molecular dynamics of the GTPase-associated center rRNA

Nucleic acids research, 2007-06, Vol.35 (12), p.4007-4017

2007

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Molecular Dynamics Simulations of Guanine Quadruplex Loops: Advances and Force Field Limitations

Biophysical journal, 2004-07, Vol.87 (1), p.227-242

2004

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Computational studies of RNA and DNA

1, 2006

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Zeitschrift / SerieThe Journal Of Physical Chemistry. A, Molecules, Spectroscopy, Kinetics, Environment, & General Theory

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Assessing the Current State of Amber Force Field Modifications for DNA

Refinement of the Sugar–Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B‑DNA

Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions

Effect of Monovalent Ion Parameters on Molecular Dynamics Simulations of G‑Quadruplexes

QM/MM Calculations on Protein–RNA Complexes: Understanding Limitations of Classical MD Simulations and Search for Reliable Cost-Effective QM Methods

Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies

Coarse-Grained Simulations Complemented by Atomistic Molecular Dynamics Provide New Insights into Folding and Unfolding of Human Telomeric G‑Quadruplexes

A- to B‑DNA Transition in AMBER Force Fields and Its Coupling to Sugar Pucker

RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview

Role of Fine Structural Dynamics in Recognition of Histone H3 by HP1γ(CSD) Dimer and Ability of Force Fields to Describe Their Interaction Network

Fine-Tuning of the AMBER RNA Force Field with a New Term Adjusting Interactions of Terminal Nucleotides

Insights into Stability and Folding of GNRA and UNCG Tetraloops Revealed by Microsecond Molecular Dynamics and Well-Tempered Metadynamics

Stability of Two-Quartet G-Quadruplexes and Their Dimers in Atomistic Simulations

Simulations of A‑RNA Duplexes. The Effect of Sequence, Solute Force Field, Water Model, and Salt Concentration

Sequential electron transfer governs the UV-induced self-repair of DNA photolesions

Reactive Conformation of the Active Site in the Hairpin Ribozyme Achieved by Molecular Dynamics Simulations with ε/ζ Force Field Reparametrizations

UV-induced hydrogen transfer in DNA base pairs promoted by dark nπ states

rRNA C‑Loops: Mechanical Properties of a Recurrent Structural Motif

How to understand quantum chemical computations on DNA and RNA systems? A practical guide for non-specialists

Solvent effects on the photochemistry of 4-aminoimidazole-5-carbonitrile, a prebiotically plausible precursor of purines

Molecular dynamics simulations of sarcin-ricin rRNA motif

Electron-driven proton transfer enables nonradiative photodeactivation in microhydrated 2-aminoimidazole

Elastic properties of ribosomal RNA building blocks: molecular dynamics of the GTPase-associated center rRNA

Molecular Dynamics Simulations of Guanine Quadruplex Loops: Advances and Force Field Limitations

Computational studies of RNA and DNA

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