Role of Mg2+Ions in DNA Hydrolysis byEcoRV, Studied by the 3D-Reference Interaction Site Model and Molecular Dynamics

The Journal of Physical Chemistry B ◽

10.1021/acs.jpcb.7b12555 ◽

2018 ◽

Vol 122 (39) ◽

pp. 9061-9075 ◽

Author(s):

Itaru Onishi ◽

Shunya Sunaba ◽

Norio Yoshida ◽

Fumio Hirata ◽

Masayuki Irisa

Keyword(s):

Molecular Dynamics ◽

Dna Hydrolysis ◽

Interaction Site ◽

Reference Interaction Site

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How Mg2+ ion and water network affect the stability and structure of non-Watson–Crick base pairs in E. coli loop E of 5S rRNA: a molecular dynamics and reference interaction site model (RISM) study

Journal of Biomolecular Structure and Dynamics ◽

10.1080/07391102.2016.1213186 ◽

2016 ◽

Vol 35 (10) ◽

pp. 2103-2122 ◽

Author(s):

Sudhanshu Shanker ◽

Pradipta Bandyopadhyay

Keyword(s):

Molecular Dynamics ◽

5S Rrna ◽

Water Network ◽

Interaction Site ◽

E Coli ◽

Reference Interaction Site ◽

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Comparison of DNA hydration patterns obtained using two distinct computational methods, molecular dynamics simulation and three-dimensional reference interaction site model theory

The Journal of Chemical Physics ◽

10.1063/1.2904865 ◽

2008 ◽

Vol 128 (18) ◽

pp. 185102 ◽

Author(s):

Yoshiteru Yonetani ◽

Yutaka Maruyama ◽

Fumio Hirata ◽

Hidetoshi Kono

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Computational Methods ◽

Model Theory ◽

Three Dimensional ◽

Dynamics Simulation ◽

Interaction Site ◽

Dna Hydration ◽

Reference Interaction Site

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Reference interaction site model and molecular dynamics study of structure and thermodynamics of methanol

The Journal of Chemical Physics ◽

10.1063/1.2803059 ◽

2007 ◽

Vol 127 (22) ◽

pp. 224501 ◽

Author(s):

D. Costa ◽

G. Munaó ◽

F. Saija ◽

C. Caccarno

Keyword(s):

Molecular Dynamics ◽

Interaction Site ◽

Reference Interaction Site

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An application of coupled reference interaction site model/molecular dynamics to the conformational analysis of the alanine dipeptide

The Journal of Chemical Physics ◽

10.1063/1.1818046 ◽

2004 ◽

Vol 121 (24) ◽

pp. 12447 ◽

Author(s):

Holly Freedman ◽

Thanh N. Truong

Keyword(s):

Molecular Dynamics ◽

Conformational Analysis ◽

Interaction Site ◽

Reference Interaction Site ◽

Alanine Dipeptide

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Publisher’s Note: “Reference interaction site model and molecular dynamics study of structure and thermodynamics of methanol” [J. Chem. Phys. 127, 224501 (2007)]

The Journal of Chemical Physics ◽

10.1063/1.2904476 ◽

2008 ◽

Vol 128 (14) ◽

pp. 149901

Author(s):

D. Costa ◽

G. Munaó ◽

F. Saija ◽

C. Caccamo

Keyword(s):

Molecular Dynamics ◽

Chem Phys ◽

Interaction Site ◽

Reference Interaction Site

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A Coupled Reference Interaction Site Model/Molecular Dynamics Study of the Potential of Mean Force Curve of the SN2 Cl-+ CH3Cl Reaction in Water

The Journal of Physical Chemistry B ◽

10.1021/jp044944c ◽

2005 ◽

Vol 109 (10) ◽

pp. 4726-4730 ◽

Author(s):

Holly Freedman ◽

Thanh N. Truong

Keyword(s):

Molecular Dynamics ◽

Potential Of Mean Force ◽

Force Curve ◽

Interaction Site ◽

Reference Interaction Site ◽

Reaction In Water

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A Study of the Tautomeric Equilibria of 2-Hydroxypyridine/2-Oxopyridine and of Cytosine in Water Using the Coupled Reference Interaction Site Model(RISM)/Molecular Dynamics (MD) Approach

The Journal of Physical Chemistry B ◽

10.1021/jp046453y ◽

2004 ◽

Vol 108 (49) ◽

pp. 19043-19048 ◽

Author(s):

Holly Freedman ◽

Hung N. Nguyen ◽

Thanh N. Truong

Keyword(s):

Molecular Dynamics ◽

Interaction Site ◽

Tautomeric Equilibria ◽

Reference Interaction Site

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Comparative Study on Solvation Free Energy Expressions in Reference Interaction Site Model Integral Equation Theory

The Journal of Physical Chemistry B ◽

10.1021/jp053259i ◽

2005 ◽

Vol 109 (36) ◽

pp. 17290-17295 ◽

Author(s):

Kazuto Sato ◽

Hiroshi Chuman ◽

Seiichiro Ten-no

Keyword(s):

Integral Equation ◽

Free Energy ◽

Comparative Study ◽

Solvation Free Energy ◽

Integral Equation Theory ◽

Interaction Site ◽

Reference Interaction Site

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Analysis of molecular dynamics simulations of 10-residue peptide, chignolin, using statistical mechanics: Relaxation mode analysis and three-dimensional reference interaction site model theory

Biophysics and Physicobiology ◽

10.2142/biophysico.16.0_407 ◽

2019 ◽

Vol 16 (0) ◽

pp. 407-429

Author(s):

Yutaka Maruyama ◽

Hiroshi Takano ◽

Ayori Mitsutake

Keyword(s):

Molecular Dynamics ◽

Statistical Mechanics ◽

Molecular Dynamics Simulations ◽

Model Theory ◽

Three Dimensional ◽

Mode Analysis ◽

Relaxation Mode ◽

Interaction Site ◽

Dynamics Simulations

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A molecular solvation theory simulation of liquid alkyl esters of acetic acid with the 3D Reference Interaction Site Model

Journal of Molecular Liquids ◽

10.1016/j.molliq.2021.117763 ◽

2021 ◽

Vol 344 ◽

pp. 117763

Author(s):

Dipankar Roy ◽

Andriy Kovalenko

Keyword(s):

Acetic Acid ◽

Alkyl Esters ◽

Interaction Site ◽

Reference Interaction Site ◽

Solvation Theory

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