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Triplex intermediates in folding of human telomeric quadruplexes probed by microsecond-scale molecular dynamics simulations

Biochimie, 2014-10, Vol.105, p.22-35

2014

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Molecular dynamics simulations of G-DNA and perspectives on the simulation of nucleic acid structures

Methods (San Diego, Calif.), 2012-05, Vol.57 (1), p.25-39

2012

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Molecular dynamics simulations reveal the parallel stranded d(GGGA)3GGG DNA quadruplex folds via multiple paths from a coil-like ensemble

International journal of biological macromolecules, 2024-03, Vol.261, p.129712-129712, Article 129712

2024

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Folding of guanine quadruplex molecules–funnel-like mechanism or kinetic partitioning? An overview from MD simulation studies

Biochimica et biophysica acta. General subjects, 2017-05, Vol.1861 (5), p.1246-1263

2017

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Composite 5-methylations of cytosines modulate i-motif stability in a sequence-specific manner: Implications for DNA nanotechnology and epigenetic regulation of plant telomeric DNA

Biochimica et biophysica acta. General subjects, 2020-09, Vol.1864 (9), p.129651, Article 129651

2020

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Solvation effects alter the photochemistry of 2-thiocytosine

Chemical physics, 2018-11, Vol.515, p.502-508

2018

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Early steps of oxidative damage in DNA quadruplexes are position-dependent: Quantum mechanical and molecular dynamics analysis of human telomeric sequence containing ionized guanine

International journal of biological macromolecules, 2022-01, Vol.194, p.882-894

2022

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Conformational dynamics of bacterial and human cytoplasmic models of the ribosomal A-site

Biochimie, 2015-05, Vol.112, p.96-110

2015

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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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Molecular dynamic simulations of protein/RNA complexes: CRISPR/Csy4 endoribonuclease

Biochimica et biophysica acta, 2015-05, Vol.1850 (5), p.1072-1090

2015

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Residues flanking the ARKme3T/S motif allow binding of diverse targets to the HP1 chromodomain: Insights from molecular dynamics simulations

Biochimica et biophysica acta. General subjects, 2021-01, Vol.1865 (1), p.129771-129771, Article 129771

2021

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Significant structural deformation of nucleic acid bases in stacked base pairs: an ab initio study beyond Hartree–Fock

Chemical physics letters, 1998-05, Vol.288 (1), p.7-14

1998

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Molecular dynamics simulations reveal the parallel stranded d(GGGA) 3 GGG DNA quadruplex folds via multiple paths from a coil-like ensemble

International journal of biological macromolecules, 2024-03, Vol.261 (Pt 2), p.129712

2024

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Residues flanking the ARK me3 T/S motif allow binding of diverse targets to the HP1 chromodomain: Insights from molecular dynamics simulations

Biochimica et biophysica acta. General subjects, 2021-01, Vol.1865 (1), p.129771

2021

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Molecular dynamics simulations and their application to four-stranded DNA

Methods (San Diego, Calif.), 2007-12, Vol.43 (4), p.278-290

2007

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Theoretical studies of RNA catalysis: Hybrid QM/MM methods and their comparison with MD and QM

Methods (San Diego, Calif.), 2009-10, Vol.49 (2), p.202-216

2009

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Sequence-dependent elastic properties of DNA

Journal of molecular biology, 2000-06, Vol.299 (3), p.695-709

2000

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Selectivity of major isoquinoline alkaloids from Chelidonium majus towards telomeric G-quadruplex: A study using a transition-FRET (t-FRET) assay

Biochimica et biophysica acta. General subjects, 2017-08, Vol.1861 (8), p.2020-2030

2017

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RNA Kink-Turns as Molecular Elbows: Hydration, Cation Binding, and Large-Scale Dynamics

Structure (London), 2006-05, Vol.14 (5), p.825-835

2006

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Intramolecular flexibility of DNA bases in adenine–thymine and guanine–cytosine Watson–Crick base pairs

Journal of molecular structure, 1999-03, Vol.477 (1), p.15-21

1999

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Unique Tertiary and Neighbor Interactions Determine Conservation Patterns of Cis Watson–Crick A/G Base-pairs

Journal of molecular biology, 2003-07, Vol.330 (5), p.967-978

2003

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Molecular dynamics of the frame-shifting pseudoknot from beet western yellows virus: the role of non-Watson-Crick base-pairing, ordered hydration, cation binding and base mutations on stability and unfolding

Journal of molecular biology, 2001-11, Vol.313 (5), p.1073-1091

2001

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Structural Dynamics of Precursor and Product of the RNA Enzyme from the Hepatitis Delta Virus as Revealed by Molecular Dynamics Simulations

Journal of molecular biology, 2005-08, Vol.351 (4), p.731-748

2005

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Thermodynamic characteristics for the formation of H-bonded DNA base pairs

Chemical physics letters, 1996-10, Vol.261 (3), p.379-384

1996

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Hydrogen bonding, stacking and cation binding of DNA bases

Journal of molecular structure. Theochem, 2001-10, Vol.573 (1), p.43-53

2001

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

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Triplex intermediates in folding of human telomeric quadruplexes probed by microsecond-scale molecular dynamics simulations

Molecular dynamics simulations of G-DNA and perspectives on the simulation of nucleic acid structures

Molecular dynamics simulations reveal the parallel stranded d(GGGA)3GGG DNA quadruplex folds via multiple paths from a coil-like ensemble

Folding of guanine quadruplex molecules–funnel-like mechanism or kinetic partitioning? An overview from MD simulation studies

Composite 5-methylations of cytosines modulate i-motif stability in a sequence-specific manner: Implications for DNA nanotechnology and epigenetic regulation of plant telomeric DNA

Solvation effects alter the photochemistry of 2-thiocytosine

Early steps of oxidative damage in DNA quadruplexes are position-dependent: Quantum mechanical and molecular dynamics analysis of human telomeric sequence containing ionized guanine

Conformational dynamics of bacterial and human cytoplasmic models of the ribosomal A-site

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

Molecular dynamic simulations of protein/RNA complexes: CRISPR/Csy4 endoribonuclease

Residues flanking the ARKme3T/S motif allow binding of diverse targets to the HP1 chromodomain: Insights from molecular dynamics simulations

Significant structural deformation of nucleic acid bases in stacked base pairs: an ab initio study beyond Hartree–Fock

Molecular dynamics simulations reveal the parallel stranded d(GGGA) 3 GGG DNA quadruplex folds via multiple paths from a coil-like ensemble

Residues flanking the ARK me3 T/S motif allow binding of diverse targets to the HP1 chromodomain: Insights from molecular dynamics simulations

Molecular dynamics simulations and their application to four-stranded DNA

Theoretical studies of RNA catalysis: Hybrid QM/MM methods and their comparison with MD and QM

Sequence-dependent elastic properties of DNA

Selectivity of major isoquinoline alkaloids from Chelidonium majus towards telomeric G-quadruplex: A study using a transition-FRET (t-FRET) assay

RNA Kink-Turns as Molecular Elbows: Hydration, Cation Binding, and Large-Scale Dynamics

Intramolecular flexibility of DNA bases in adenine–thymine and guanine–cytosine Watson–Crick base pairs

Unique Tertiary and Neighbor Interactions Determine Conservation Patterns of Cis Watson–Crick A/G Base-pairs

Molecular dynamics of the frame-shifting pseudoknot from beet western yellows virus: the role of non-Watson-Crick base-pairing, ordered hydration, cation binding and base mutations on stability and unfolding

Structural Dynamics of Precursor and Product of the RNA Enzyme from the Hepatitis Delta Virus as Revealed by Molecular Dynamics Simulations

Thermodynamic characteristics for the formation of H-bonded DNA base pairs

Hydrogen bonding, stacking and cation binding of DNA bases

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