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Dynamics of strand slippage in DNA hairpins formed by CAG repeats: roles of sequence parity and trinucleotide interrupts

Nucleic acids research, 2020-03, Vol.48 (5), p.2232-2245

2020

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Classical Electrostatics for Biomolecular Simulations

Chemical reviews, 2014-01, Vol.114 (1), p.779-814

2014

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Atypical structures of GAA/TTC trinucleotide repeats underlying Friedreich’s ataxia: DNA triplexes and RNA/DNA hybrids

Nucleic acids research, 2020-09, Vol.48 (17), p.9899-9917

2020

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Ion distributions around left- and right-handed DNA and RNA duplexes: a comparative study

Nucleic acids research, 2014-12, Vol.42 (22), p.13981-13996

2014

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Adaptively biased molecular dynamics for free energy calculations

The Journal of chemical physics, 2008-04, Vol.128 (13), p.134101-134101-7

2008

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Secondary structure assignment for conformationally irregular peptides: Comparison between DSSP, STRIDE and KAKSI

Journal of molecular graphics & modelling, 2015-02, Vol.55, p.72-84

2015

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Pathologic polyglutamine aggregation begins with a self-poisoning polymer crystal

eLife, 2023-11, Vol.12

2023

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Investigating rare events with nonequilibrium work measurements. II. Transition and reaction rates

The Journal of chemical physics, 2014-01, Vol.140 (3), p.034115-034115

2014

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Investigating rare events with nonequilibrium work measurements. I. Nonequilibrium transition path probabilities

The Journal of chemical physics, 2014-01, Vol.140 (3), p.034114-034114

2014

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Conformations and free energy landscapes of polyproline peptides

Proceedings of the National Academy of Sciences - PNAS, 2009-12, Vol.106 (49), p.20746-20751

2009

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Comparative melting and healing of B-DNA and Z-DNA by an infrared laser pulse

The Journal of chemical physics, 2016-04, Vol.144 (14), p.145101-145101

2016

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Publisher's Note: “Investigating rare events with nonequilibrium work measurements. I. Nonequilibrium transition path probabilities” [J. Chem. Phys. 140, 034114 (2014)]

The Journal of chemical physics, 2014-02, Vol.140 (6)

2014

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Picosecond dissociation of amyloid fibrils with infrared laser: A nonequilibrium simulation study

The Journal of chemical physics, 2015-10, Vol.143 (15), p.155101-155101

2015

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Amyloid Properties of Asparagine and Glutamine in Prion-like Proteins

ACS chemical neuroscience, 2016-05, Vol.7 (5), p.576-587

2016

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Efficient particle-mesh Ewald based approach to fixed and induced dipolar interactions

The Journal of chemical physics, 2000-12, Vol.113 (24), p.10913-10927

2000

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Towards an accurate representation of electrostatics in classical force fields: efficient implementation of multipolar interactions in biomolecular simulations

The Journal of chemical physics, 2004-01, Vol.120 (1), p.73-87

2004

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Construction of DNA/RNA Triplex Helices Based on GAA/TTC Trinucleotide Repeats

Bio-protocol, 2021-09, Vol.11 (18), p.e4155-e4155

2021

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Molecular conformations and dynamics of nucleotide repeats associated with neurodegenerative diseases: double helices and CAG hairpin loops

Computational and structural biotechnology journal, 2021-01, Vol.19, p.2819-2832

2021

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Are long-range structural correlations behind the aggregration phenomena of polyglutamine diseases?

PLoS computational biology, 2012-04, Vol.8 (4), p.e1002501-e1002501

2012

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Binding polymorphism in the DNA bound state of the Pdx1 homeodomain

PLoS computational biology, 2013-08, Vol.9 (8), p.e1003160-e1003160

2013

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Picosecond melting of peptide nanotubes using an infrared laser: a nonequilibrium simulation study

Physical chemistry chemical physics : PCCP, 2015-01, Vol.17 (41), p.27275-27280

2015

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Novel eGZ-motif formed by regularly extruded guanine bases in a left-handed Z-DNA helix as a major motif behind CGG trinucleotide repeats

Nucleic acids research, 2022-05, Vol.50 (9), p.4860-4876

2022

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Structure and Dynamics of DNA and RNA Double Helices Formed by d(CTG), d(GTC), r(CUG), and r(GUC) Trinucleotide Repeats and Associated DNA–RNA Hybrids

The journal of physical chemistry. B, 2023-09, Vol.127 (37), p.7907-7924

2023

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Conformational free energies of methyl-alpha-L-iduronic and methyl-beta-D-glucuronic acids in water

The Journal of chemical physics, 2010-03, Vol.132 (10), p.104108-104108

2010

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Deprotonation of Solvated Formic Acid: Car−Parrinello and Metadynamics Simulations

The journal of physical chemistry. B, 2006-02, Vol.110 (5), p.2325-2331

2006

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Dynamics of strand slippage in DNA hairpins formed by CAG repeats: roles of sequence parity and trinucleotide interrupts

Classical Electrostatics for Biomolecular Simulations

Atypical structures of GAA/TTC trinucleotide repeats underlying Friedreich’s ataxia: DNA triplexes and RNA/DNA hybrids

Ion distributions around left- and right-handed DNA and RNA duplexes: a comparative study

Adaptively biased molecular dynamics for free energy calculations

Secondary structure assignment for conformationally irregular peptides: Comparison between DSSP, STRIDE and KAKSI

Pathologic polyglutamine aggregation begins with a self-poisoning polymer crystal

Investigating rare events with nonequilibrium work measurements. II. Transition and reaction rates

Investigating rare events with nonequilibrium work measurements. I. Nonequilibrium transition path probabilities

Conformations and free energy landscapes of polyproline peptides

Comparative melting and healing of B-DNA and Z-DNA by an infrared laser pulse

Publisher's Note: “Investigating rare events with nonequilibrium work measurements. I. Nonequilibrium transition path probabilities” [J. Chem. Phys. 140, 034114 (2014)]

Picosecond dissociation of amyloid fibrils with infrared laser: A nonequilibrium simulation study

Amyloid Properties of Asparagine and Glutamine in Prion-like Proteins

Efficient particle-mesh Ewald based approach to fixed and induced dipolar interactions

Towards an accurate representation of electrostatics in classical force fields: efficient implementation of multipolar interactions in biomolecular simulations

Construction of DNA/RNA Triplex Helices Based on GAA/TTC Trinucleotide Repeats

Molecular conformations and dynamics of nucleotide repeats associated with neurodegenerative diseases: double helices and CAG hairpin loops

Are long-range structural correlations behind the aggregration phenomena of polyglutamine diseases?

Binding polymorphism in the DNA bound state of the Pdx1 homeodomain

Picosecond melting of peptide nanotubes using an infrared laser: a nonequilibrium simulation study

Novel eGZ-motif formed by regularly extruded guanine bases in a left-handed Z-DNA helix as a major motif behind CGG trinucleotide repeats

Structure and Dynamics of DNA and RNA Double Helices Formed by d(CTG), d(GTC), r(CUG), and r(GUC) Trinucleotide Repeats and Associated DNA–RNA Hybrids

Conformational free energies of methyl-alpha-L-iduronic and methyl-beta-D-glucuronic acids in water

Deprotonation of Solvated Formic Acid: Car−Parrinello and Metadynamics Simulations

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