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Calculating Structures and Free Energies of Complex Molecules: Combining Molecular Mechanics and Continuum Models

Accounts of chemical research, 2000-12, Vol.33 (12), p.889-897

2000

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Molecular dynamics simulation of nucleic acids: Successes, limitations, and promise

Biopolymers, 2000, Vol.56 (4), p.232-256

2000

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Molecular Dynamics Simulations on Solvated Biomolecular Systems: The Particle Mesh Ewald Method Leads to Stable Trajectories of DNA, RNA, and Proteins

Journal of the American Chemical Society, 1995-04, Vol.117 (14), p.4193-4194

1995

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Structural dynamics of possible late-stage intermediates in folding of quadruplex DNA studied by molecular simulations

Nucleic acids research, 2013-08, Vol.41 (14), p.7128-7143

2013

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Observation of the A-DNA to B-DNA Transition During Unrestrained Molecular Dynamics in Aqueous Solution

Journal of molecular biology, 1996-06, Vol.259 (3), p.434-444

1996

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Molecular dynamics simulation of nucleic acids

Annual review of physical chemistry, 2000-01, Vol.51 (1), p.435-471

2000

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A Modified Version of the Cornell et al. Force Field with Improved Sugar Pucker Phases and Helical Repeat

Journal of biomolecular structure & dynamics, 1999-02, Vol.16 (4), p.845-862

1999

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Dissociative reactions of benzonorbornadienes with tetrazines: scope of leaving groups and mechanistic insights

Organic & biomolecular chemistry, 2017, Vol.15 (46), p.9855-9865

2017

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Development of an informatics infrastructure for data exchange of biomolecular simulations: Architecture, data models and ontology

SAR and QSAR in environmental research, 2015-09, Vol.26 (7-9), p.577-593

2015

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Molecular Dynamics and Continuum Solvent Studies of the Stability of PolyG-PolyC and PolyA-PolyT DNA Duplexes in Solution

Journal of biomolecular structure & dynamics, 1998-10, Vol.16 (2), p.265-280

1998

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A Molecular Level Picture of the Stabilization of A-DNA in Mixed Ethanol--Water Solutions

Proceedings of the National Academy of Sciences - PNAS, 1997-09, Vol.94 (18), p.9626-9630

1997

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Molecular Dynamics Simulations Find That 3‘ Phosphoramidate Modified DNA Duplexes Undergo a B to A Transition and Normal DNA Duplexes an A to B Transition

Journal of the American Chemical Society, 1997-07, Vol.119 (29), p.6722-6730

1997

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Continuum Solvent Studies of the Stability of DNA, RNA, and Phosphoramidate−DNA Helices

Journal of the American Chemical Society, 1998-09, Vol.120 (37), p.9401-9409

1998

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Intercalation processes of copper complexes in DNA

Nucleic acids research, 2015-06, Vol.43 (11), p.5364-5376

2015

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Molecular Dynamics Simulations and Thermodynamics Analysis of DNA−Drug Complexes. Minor Groove Binding between 4‘,6-Diamidino-2-phenylindole and DNA Duplexes in Solution

Journal of the American Chemical Society, 2003-02, Vol.125 (7), p.1759-1769

2003

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Restrained molecular dynamics of solvated duplex DNA using the particle mesh Ewald method

Journal of biomolecular NMR, 1999-02, Vol.13 (2), p.119-131

1999

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Insight into the stabilization of A-DNA by specific ion association: spontaneous B-DNA to A-DNA transitions observed in molecular dynamics simulations of d[ACCCGCGGGT] 2 in the presence of hexaamminecobalt(III)

Structure (London), 1997-10, Vol.5 (10), p.1297-1311

1997

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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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DNA Deformability at the Base Pair Level

Journal of the American Chemical Society, 2004-04, Vol.126 (13), p.4124-4125

2004

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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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The Amber biomolecular simulation programs

Journal of computational chemistry, 2005-12, Vol.26 (16), p.1668-1688

2005

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Dissociative reactions of benzonorbornadienes with tetrazines: scope of leaving groups and mechanistic insightsElectronic supplementary information (ESI) available: Detailed experimental procedures, supporting figures, and tables. See DOI: 10.1039/c7ob02191g

2017-11

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Molecular Modeling of Nucleic Acid Structure: Electrostatics and Solvation

Current Protocols in Nucleic Acid Chemistry, 2001-08, Vol.5 (1), p.7.9.1-7.9.21

2001

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Simulation and modeling of nucleic acid structure, dynamics and interactions

Current opinion in structural biology, 2004-06, Vol.14 (3), p.360-367

Cheatham, Thomas E

2004

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Molecular Dynamics Simulations of the 136 Unique Tetranucleotide Sequences of DNA Oligonucleotides. II: Sequence Context Effects on the Dynamical Structures of the 10 Unique Dinucleotide Steps

Biophysical journal, 2005-12, Vol.89 (6), p.3721-3740

2005

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Calculating Structures and Free Energies of Complex Molecules: Combining Molecular Mechanics and Continuum Models

Molecular dynamics simulation of nucleic acids: Successes, limitations, and promise

Molecular Dynamics Simulations on Solvated Biomolecular Systems: The Particle Mesh Ewald Method Leads to Stable Trajectories of DNA, RNA, and Proteins

Structural dynamics of possible late-stage intermediates in folding of quadruplex DNA studied by molecular simulations

Observation of the A-DNA to B-DNA Transition During Unrestrained Molecular Dynamics in Aqueous Solution

Molecular dynamics simulation of nucleic acids

A Modified Version of the Cornell et al. Force Field with Improved Sugar Pucker Phases and Helical Repeat

Dissociative reactions of benzonorbornadienes with tetrazines: scope of leaving groups and mechanistic insights

Development of an informatics infrastructure for data exchange of biomolecular simulations: Architecture, data models and ontology

Molecular Dynamics and Continuum Solvent Studies of the Stability of PolyG-PolyC and PolyA-PolyT DNA Duplexes in Solution

A Molecular Level Picture of the Stabilization of A-DNA in Mixed Ethanol--Water Solutions

Molecular Dynamics Simulations Find That 3‘ Phosphoramidate Modified DNA Duplexes Undergo a B to A Transition and Normal DNA Duplexes an A to B Transition

Continuum Solvent Studies of the Stability of DNA, RNA, and Phosphoramidate−DNA Helices

Intercalation processes of copper complexes in DNA

Molecular Dynamics Simulations and Thermodynamics Analysis of DNA−Drug Complexes. Minor Groove Binding between 4‘,6-Diamidino-2-phenylindole and DNA Duplexes in Solution

Restrained molecular dynamics of solvated duplex DNA using the particle mesh Ewald method

Insight into the stabilization of A-DNA by specific ion association: spontaneous B-DNA to A-DNA transitions observed in molecular dynamics simulations of d[ACCCGCGGGT] 2 in the presence of hexaamminecobalt(III)

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

DNA Deformability at the Base Pair Level

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

The Amber biomolecular simulation programs

Dissociative reactions of benzonorbornadienes with tetrazines: scope of leaving groups and mechanistic insightsElectronic supplementary information (ESI) available: Detailed experimental procedures, supporting figures, and tables. See DOI: 10.1039/c7ob02191g

Molecular Modeling of Nucleic Acid Structure: Electrostatics and Solvation

Simulation and modeling of nucleic acid structure, dynamics and interactions

Molecular Dynamics Simulations of the 136 Unique Tetranucleotide Sequences of DNA Oligonucleotides. II: Sequence Context Effects on the Dynamical Structures of the 10 Unique Dinucleotide Steps

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