Locating missing water molecules in protein cavities by the three-dimensional reference interaction site model theory of molecular solvation

Takashi Imai; Ryusuke Hiraoka; Andriy Kovalenko; Fumio Hirata

doi:10.1002/prot.21311

Locating missing water molecules in protein cavities by the three-dimensional reference interaction site model theory of molecular solvation

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.21311 ◽

2006 ◽

Vol 66 (4) ◽

pp. 804-813 ◽

Cited By ~ 65

Author(s):

Takashi Imai ◽

Ryusuke Hiraoka ◽

Andriy Kovalenko ◽

Fumio Hirata

Keyword(s):

Model Theory ◽

Three Dimensional ◽

Water Molecules ◽

Interaction Site ◽

Site Model ◽

Reference Interaction Site

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Tip-sample interaction force mediated by water molecules for AFM in water: Three-dimensional reference interaction site model theory

Physical Review B ◽

10.1103/physrevb.82.035414 ◽

2010 ◽

Vol 82 (3) ◽

Cited By ~ 19

Author(s):

Masanori Harada ◽

Masaru Tsukada

Keyword(s):

Model Theory ◽

Three Dimensional ◽

Interaction Force ◽

Water Molecules ◽

Interaction Site ◽

Site Model ◽

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 ◽

Cited By ~ 12

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 ◽

Site Model ◽

Dna Hydration ◽

Reference Interaction Site

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Development of a solvent-polarizable three-dimensional reference interaction-site model theory

The Journal of Chemical Physics ◽

10.1063/5.0004173 ◽

2020 ◽

Vol 152 (11) ◽

pp. 114108 ◽

Cited By ~ 1

Author(s):

Norio Yoshida ◽

Tsuyoshi Yamaguchi

Keyword(s):

Model Theory ◽

Three Dimensional ◽

Interaction Site ◽

Site Model ◽

Reference Interaction Site

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Erratum: “Development of a solvent-polarizable three-dimensional reference interaction-site model theory” [J. Chem. Phys. 152, 114108 (2020)]

The Journal of Chemical Physics ◽

10.1063/5.0010622 ◽

2020 ◽

Vol 152 (18) ◽

pp. 189904

Author(s):

Norio Yoshida ◽

Tsuyoshi Yamaguchi

Keyword(s):

Model Theory ◽

Three Dimensional ◽

Chem Phys ◽

Interaction Site ◽

Site Model ◽

Reference Interaction Site

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Partial Molar Volume of Proteins Studied by the Three-Dimensional Reference Interaction Site Model Theory†

The Journal of Physical Chemistry B ◽

10.1021/jp045667c ◽

2005 ◽

Vol 109 (14) ◽

pp. 6658-6665 ◽

Cited By ~ 38

Author(s):

Takashi Imai ◽

Andriy Kovalenko ◽

Fumio Hirata

Keyword(s):

Molar Volume ◽

Partial Molar Volume ◽

Model Theory ◽

Three Dimensional ◽

Interaction Site ◽

Site Model ◽

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 ◽

Site Model ◽

Dynamics Simulations

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Solvation structure, thermodynamics, and conformational dependence of alanine dipeptide in aqueous solution analyzed with reference interaction site model theory

The Journal of Chemical Physics ◽

10.1063/1.1524617 ◽

2003 ◽

Vol 118 (1) ◽

pp. 279-290 ◽

Cited By ~ 8

Author(s):

Qizhi Cui ◽

Vedene H. Smith

Keyword(s):

Aqueous Solution ◽

Model Theory ◽

Interaction Site ◽

Site Model ◽

Solvation Structure ◽

Reference Interaction Site ◽

Alanine Dipeptide

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Solute-structure dependence of solvation dynamics studied by reference interaction-site model theory

The Journal of Chemical Physics ◽

10.1063/1.1532345 ◽

2003 ◽

Vol 118 (5) ◽

pp. 2279-2285 ◽

Cited By ~ 13

Author(s):

Katsura Nishiyama ◽

Fumio Hirata ◽

Tadashi Okada

Keyword(s):

Model Theory ◽

Solvation Dynamics ◽

Structure Dependence ◽

Interaction Site ◽

Site Model ◽

Reference Interaction Site

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Solvation free-energy pressure corrections in the three dimensional reference interaction site model

The Journal of Chemical Physics ◽

10.1063/1.4935065 ◽

2015 ◽

Vol 143 (18) ◽

pp. 184116 ◽

Cited By ~ 38

Author(s):

Volodymyr Sergiievskyi ◽

Guillaume Jeanmairet ◽

Maximilien Levesque ◽

Daniel Borgis

Keyword(s):

Free Energy ◽

Three Dimensional ◽

Solvation Free Energy ◽

Interaction Site ◽

Site Model ◽

Reference Interaction Site

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Thermodynamically consistent reference interaction site model theory of the tangent diatomic fluid

Chemical Physics Letters ◽

10.1016/j.cplett.2009.01.064 ◽

2009 ◽

Vol 470 (4-6) ◽

pp. 240-243 ◽

Cited By ~ 13

Author(s):

G. Munaò ◽

D. Costa ◽

C. Caccamo

Keyword(s):

Model Theory ◽

Interaction Site ◽

Site Model ◽

Reference Interaction Site

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