Sequence-Dependent Conformational Energy of DNA Derived from Molecular Dynamics Simulations:  Toward Understanding the Indirect Readout Mechanism in Protein−DNA Recognition

2005 ◽  
Vol 127 (46) ◽  
pp. 16074-16089 ◽  
Author(s):  
Marcos J. Araúzo-Bravo ◽  
Satoshi Fujii ◽  
Hidetoshi Kono ◽  
Shandar Ahmad ◽  
Akinori Sarai
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Dna Recognition ◽  
Conformational Energy ◽  
Sequence Dependent ◽  
Dynamics Simulations ◽  
Indirect Readout

scholarly journals 2P119 Indirect readout in protein-DNA recognition : evaluation of conformational energy of DNA from molecular dynamics simulations

2004 ◽  
Vol 44 (supplement) ◽  
pp. S139
Author(s):  
Marcos J. Arauzo-Bravo ◽  
Shandar Ahmad ◽  
S. Fujii ◽  
S. Takenaka ◽  
H. Kono ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Dna Recognition ◽  
Conformational Energy ◽  
Dynamics Simulations ◽  
Indirect Readout

scholarly journals Sequence-dependent DNA deformability studied using molecular dynamics simulations

2007 ◽  
Vol 35 (18) ◽  
pp. 6063-6074 ◽  
Author(s):  
Satoshi Fujii ◽  
Hidetoshi Kono ◽  
Shigeori Takenaka ◽  
Nobuhiro Go ◽  
Akinori Sarai
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Sequence Dependent ◽  
Dynamics Simulations

scholarly journals 2P145 Molecular Dynamics Simulations of DNA : Application to the Specificity of Protein-DNA Recognition

2005 ◽  
Vol 45 (supplement) ◽  
pp. S156
Author(s):  
Marcos Arauzo-Bravo ◽  
H. Kono ◽  
S. Fujii ◽  
A. Sarai
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Dna Recognition ◽  
Dynamics Simulations

scholarly journals Sequence-dependent mechanical properties of double-stranded RNA

Nanoscale ◽  
2019 ◽  
Vol 11 (44) ◽  
pp. 21471-21478 ◽  
Author(s):  
Alberto Marin-Gonzalez ◽  
J. G. Vilhena ◽  
Fernando Moreno-Herrero ◽  
Ruben Perez
Keyword(s):  
Mechanical Properties ◽  
Molecular Dynamics ◽  
Nucleotide Sequence ◽  
Molecular Dynamics Simulations ◽  
Mechanical Response ◽  
Double Stranded Rna ◽  
Sequence Dependent ◽  
Dynamics Simulations

Atomistic molecular dynamics simulations reveal the strikingly different effect of the nucleotide sequence on the mechanical response of dsRNA and dsDNA.

scholarly journals A generalized conformational energy function of DNA derived from molecular dynamics simulations

2009 ◽  
Vol 37 (20) ◽  
pp. e135-e135 ◽  
Author(s):  
S. Yamasaki ◽  
T. Terada ◽  
K. Shimizu ◽  
H. Kono ◽  
A. Sarai
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Energy Function ◽  
Conformational Energy ◽  
Dynamics Simulations
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