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Ion Motions in Molecular Dynamics Simulations on DNA

Proceedings of the National Academy of Sciences - PNAS, 2004-10, Vol.101 (41), p.14771-14775

2004

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The ABCs of molecular dynamics simulations on B-DNA, circa 2012

Journal of biosciences, 2012-07, Vol.37 (3), p.379-397

2012

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U1A protein-stem loop 2 RNA recognition: Prediction of structural differences from protein mutations

Biopolymers, 2011-09, Vol.95 (9), p.591-606

2011

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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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Molecular Dynamics Simulations of the 136 Unique Tetranucleotide Sequences of DNA Oligonucleotides. I. Research Design and Results on d(C pG) Steps

Biophysical journal, 2004-12, Vol.87 (6), p.3799-3813

2004

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Nucleic acids: theory and computer simulation, Y2K

Current Opinion in Structural Biology, 2000-04, Vol.10 (2), p.182-196

2000

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Studies of base pair sequence effects on DNA solvation based on all-atom molecular dynamics simulations

Journal of biosciences, 2012-07, Vol.37 (3), p.399-421

2012

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Identification of an Aminoacridine Derivative That Binds to RNA Tetraloops

Journal of medicinal chemistry, 2007-08, Vol.50 (17), p.4096-4104

2007

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Structural bioinformatics of DNA: a web-based tool for the analysis of molecular dynamics results and structure prediction

Bioinformatics, 2006-04, Vol.22 (8), p.1007-1009

2006

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Axis Curvature and Ligand Induced Bending in the CAP-DNA Oligomers

Biophysical journal, 2005-01, Vol.88 (1), p.L04-L06

2005

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Toward a Dynamical Structure of DNA: Comparison of Theoretical and Experimental NOE Intensities

Science (American Association for the Advancement of Science), 1992-01, Vol.255 (5044), p.597-599

1992

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Molecular dynamics simulation reveals sequence-intrinsic and protein-induced geometrical features of the OL1 DNA operator

Biopolymers, 2001-10, Vol.59 (4), p.205-225

2001

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Conformational Properties of the TATA-Box Binding Sequence of DNA

Journal of biomolecular structure & dynamics, 1997-06, Vol.14 (6), p.757-765

1997

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[5] Structure determination and analysis of local bending in an A-tract DNA duplex: Comparison of results from crystallography, nuclear magnetic resonance, and molecular dynamics simulation on d(CGCAAAAATGCG)

Methods in Enzymology, 1995, Vol.261, p.121,IN1,129-128,IN2,144

1995

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HADHB, HuR, and CP1 Bind to the Distal 3′-Untranslated Region of Human Renin mRNA and Differentially Modulate Renin Expression

The Journal of biological chemistry, 2003-11, Vol.278 (45), p.44894-44903

2003

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Ion Motions in Molecular Dynamics Simulations on DNA

The ABCs of molecular dynamics simulations on B-DNA, circa 2012

U1A protein-stem loop 2 RNA recognition: Prediction of structural differences from protein mutations

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

Molecular Dynamics Simulations of the 136 Unique Tetranucleotide Sequences of DNA Oligonucleotides. I. Research Design and Results on d(C pG) Steps

Nucleic acids: theory and computer simulation, Y2K

Studies of base pair sequence effects on DNA solvation based on all-atom molecular dynamics simulations

Identification of an Aminoacridine Derivative That Binds to RNA Tetraloops

Structural bioinformatics of DNA: a web-based tool for the analysis of molecular dynamics results and structure prediction

Axis Curvature and Ligand Induced Bending in the CAP-DNA Oligomers

Toward a Dynamical Structure of DNA: Comparison of Theoretical and Experimental NOE Intensities

Molecular dynamics simulation reveals sequence-intrinsic and protein-induced geometrical features of the OL1 DNA operator

Conformational Properties of the TATA-Box Binding Sequence of DNA

[5] Structure determination and analysis of local bending in an A-tract DNA duplex: Comparison of results from crystallography, nuclear magnetic resonance, and molecular dynamics simulation on d(CGCAAAAATGCG)

HADHB, HuR, and CP1 Bind to the Distal 3′-Untranslated Region of Human Renin mRNA and Differentially Modulate Renin Expression

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