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Geometrical and Electronic Structure Variability of the Sugar−phosphate Backbone in Nucleic Acids

The journal of physical chemistry. B, 2008-07, Vol.112 (27), p.8188-8197

2008

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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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Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles

Journal of chemical theory and computation, 2011-09, Vol.7 (9), p.2886-2902

2011

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High-energy chemistry of formamide: A unified mechanism of nucleobase formation

Proceedings of the National Academy of Sciences - PNAS, 2015-01, Vol.112 (3), p.657-662

2015

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Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters

Journal of chemical theory and computation, 2013-05, Vol.9 (5), p.2339-2354

2013

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Free Energy Landscape of GAGA and UUCG RNA Tetraloops

The journal of physical chemistry letters, 2016-10, Vol.7 (20), p.4032-4038

2016

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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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Base Pair Fraying in Molecular Dynamics Simulations of DNA and RNA

Journal of chemical theory and computation, 2014-08, Vol.10 (8), p.3177-3189

2014

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Comparison of Intrinsic Stacking Energies of Ten Unique Dinucleotide Steps in A-RNA and B-DNA Duplexes. Can We Determine Correct Order of Stability by Quantum-Chemical Calculations?

The journal of physical chemistry. B, 2010-01, Vol.114 (2), p.1191-1203

2010

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Z‑DNA as a Touchstone for Additive Empirical Force Fields and a Refinement of the Alpha/Gamma DNA Torsions for AMBER

Journal of chemical theory and computation, 2021-10, Vol.17 (10), p.6292-6301

2021

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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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Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins

Journal of chemical theory and computation, 2010-12, Vol.6 (12), p.3836-3849

2010

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Surprisingly broad applicability of the cc-pVnZ-F12 basis set for ground and excited states

The Journal of chemical physics, 2020-06, Vol.152 (21), p.214104-214104

2020

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Nature and magnitude of aromatic base stacking in DNA and RNA: Quantum chemistry, molecular mechanics, and experiment

Biopolymers, 2013-12, Vol.99 (12), p.978-988

2013

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Emergence of the First Catalytic Oligonucleotides in a Formamide-Based Origin Scenario

Chemistry : a European journal, 2016-03, Vol.22 (11), p.3572-3586

2016

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Conformational Heterogeneity of RNA Stem-Loop Hairpins Bound to FUS-RNA Recognition Motif with Disordered RGG Tail Revealed by Unbiased Molecular Dynamics Simulations

The journal of physical chemistry. B, 2022-11, Vol.126 (45), p.9207-9221

2022

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2,6-diaminopurine promotes repair of DNA lesions under prebiotic conditions

Nature communications, 2021-05, Vol.12 (1), p.3018-3018, Article 3018

2021

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Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome

The journal of physical chemistry letters, 2014-05, Vol.5 (10), p.1771-1782

2014

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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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Mechanical Stability and Unfolding Pathways of Parallel Tetrameric G‑Quadruplexes Probed by Pulling Simulations

Journal of chemical information and modeling, 2024-05, Vol.64 (9), p.3896-3911

2024

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Nature and magnitude of aromatic stacking of nucleic acid bases

Physical chemistry chemical physics : PCCP, 2008-01, Vol.10 (19), p.2595-2610

2008

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On the Road from Formamide Ices to Nucleobases: IR-Spectroscopic Observation of a Direct Reaction between Cyano Radicals and Formamide in a High-Energy Impact Event

Journal of the American Chemical Society, 2012-12, Vol.134 (51), p.20788-20796

2012

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Molecular basis for AU-rich element recognition and dimerization by the HuR C-terminal RRM

Proceedings of the National Academy of Sciences - PNAS, 2019-02, Vol.116 (8), p.2935-2944

2019

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Acid‐Catalyzed RNA‐Oligomerization from 3’,5’‐cGMP

Chemistry : a European journal, 2021-12, Vol.27 (70), p.17581-17585

2021

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Geometrical and Electronic Structure Variability of the Sugar−phosphate Backbone in Nucleic Acids

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

Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles

High-energy chemistry of formamide: A unified mechanism of nucleobase formation

Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters

Free Energy Landscape of GAGA and UUCG RNA Tetraloops

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

Base Pair Fraying in Molecular Dynamics Simulations of DNA and RNA

Comparison of Intrinsic Stacking Energies of Ten Unique Dinucleotide Steps in A-RNA and B-DNA Duplexes. Can We Determine Correct Order of Stability by Quantum-Chemical Calculations?

Z‑DNA as a Touchstone for Additive Empirical Force Fields and a Refinement of the Alpha/Gamma DNA Torsions for AMBER

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

Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins

Surprisingly broad applicability of the cc-pVnZ-F12 basis set for ground and excited states

Nature and magnitude of aromatic base stacking in DNA and RNA: Quantum chemistry, molecular mechanics, and experiment

Emergence of the First Catalytic Oligonucleotides in a Formamide-Based Origin Scenario

Conformational Heterogeneity of RNA Stem-Loop Hairpins Bound to FUS-RNA Recognition Motif with Disordered RGG Tail Revealed by Unbiased Molecular Dynamics Simulations

2,6-diaminopurine promotes repair of DNA lesions under prebiotic conditions

Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome

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

Mechanical Stability and Unfolding Pathways of Parallel Tetrameric G‑Quadruplexes Probed by Pulling Simulations

Nature and magnitude of aromatic stacking of nucleic acid bases

On the Road from Formamide Ices to Nucleobases: IR-Spectroscopic Observation of a Direct Reaction between Cyano Radicals and Formamide in a High-Energy Impact Event

Molecular basis for AU-rich element recognition and dimerization by the HuR C-terminal RRM

Acid‐Catalyzed RNA‐Oligomerization from 3’,5’‐cGMP

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