3P070 Multi-scale free energy calculation method with the combination of coarse-grained and all-atom models.(Protein: Property,The 48th Annual Meeting of the Biophysical Society of Japan)

Ryuhei Harada; Akio Kitao

doi:10.2142/biophys.50.s157_2

3P070 Multi-scale free energy calculation method with the combination of coarse-grained and all-atom models.(Protein: Property,The 48th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.50.s157_2 ◽

2010 ◽

Vol 50 (supplement2) ◽

pp. S157

Author(s):

Ryuhei Harada ◽

Akio Kitao

Keyword(s):

Free Energy ◽

Annual Meeting ◽

Calculation Method ◽

Coarse Grained ◽

Free Energy Calculation ◽

Energy Calculation ◽

Scale Free ◽

Multi Scale ◽

Protein Property ◽

Biophysical Society

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3P-011 Development of the free energy calculation method using a Brownian Dynamics/Umbrella Sampling(The 46th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.48.s129_4 ◽

2008 ◽

Vol 48 (supplement) ◽

pp. S129

Author(s):

Wankee Kim ◽

Tadashi Ando ◽

Ichiro Yamato

Keyword(s):

Free Energy ◽

Annual Meeting ◽

Calculation Method ◽

Brownian Dynamics ◽

Umbrella Sampling ◽

Free Energy Calculation ◽

Energy Calculation ◽

Biophysical Society

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Multi-Scale Free Energy Landscape calculation method by combination of coarse-grained and all-atom models

Chemical Physics Letters ◽

10.1016/j.cplett.2011.01.017 ◽

2011 ◽

Vol 503 (1-3) ◽

pp. 145-152 ◽

Cited By ~ 9

Author(s):

Ryuhei Harada ◽

Akio Kitao

Keyword(s):

Free Energy ◽

Calculation Method ◽

Energy Landscape ◽

Coarse Grained ◽

Free Energy Landscape ◽

Scale Free ◽

Multi Scale

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Erratum to ‘Multi-Scale Free Energy Landscape calculation method by combination of coarse-grained and all-atom models’ [Chem. Phys. Lett. 503 (2011) 145–152]

Chemical Physics Letters ◽

10.1016/j.cplett.2011.09.006 ◽

2011 ◽

Vol 516 (1-3) ◽

pp. 113 ◽

Cited By ~ 8

Author(s):

Ryuhei Harada ◽

Akio Kitao

Keyword(s):

Free Energy ◽

Calculation Method ◽

Energy Landscape ◽

Chem Phys ◽

Coarse Grained ◽

Free Energy Landscape ◽

Scale Free ◽

Multi Scale

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3P-134 Estimation of ligand binding free energies of F-ATPase by using molecular dynamics/free energy calculation(The 46th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.48.s148_3 ◽

2008 ◽

Vol 48 (supplement) ◽

pp. S148

Author(s):

Atsushi Suenaga ◽

Osamu Umezu ◽

Tadashi Ando ◽

Ichiro Yamato ◽

Takeshi Murata ◽

...

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Ligand Binding ◽

Annual Meeting ◽

Free Energy Calculation ◽

Energy Calculation ◽

Free Energies ◽

Biophysical Society ◽

Binding Free Energies

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1PS020 Free energy calculation of lever-arm swing of myosin and the effect of actin filament(The 50th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.52.s77_3 ◽

2012 ◽

Vol 52 (supplement) ◽

pp. S77

Author(s):

Jun Ohnuki ◽

Takato Sato ◽

Koji Umezawa ◽

Mitsunori Takano

Keyword(s):

Free Energy ◽

Annual Meeting ◽

Actin Filament ◽

Free Energy Calculation ◽

Energy Calculation ◽

Arm Swing ◽

Lever Arm ◽

Biophysical Society

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1P037 Integrated Hamiltonian Sampling: towards efficient free energy calculation and conformational sampling(01B. Protein : Structure & Function,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))

Seibutsu Butsuri ◽

10.2142/biophys.54.s147_1 ◽

2014 ◽

Vol 54 (supplement1-2) ◽

pp. S147

Author(s):

Toshifumi Mori ◽

Qiang Cui

Keyword(s):

Free Energy ◽

Protein Structure ◽

Structure Function ◽

Annual Meeting ◽

Free Energy Calculation ◽

Conformational Sampling ◽

Energy Calculation ◽

Biophysical Society

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3P055 Improved Multi-Replica Metadynamics for Free Energy Calculations(01C. Protein: Property,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))

Seibutsu Butsuri ◽

10.2142/biophys.54.s258_1 ◽

2014 ◽

Vol 54 (supplement1-2) ◽

pp. S258

Author(s):

Raimondas Galvelis ◽

Yuji Sugita

Keyword(s):

Free Energy ◽

Annual Meeting ◽

Free Energy Calculations ◽

Energy Calculations ◽

Protein Property ◽

Biophysical Society

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Analyzing the robustness of the MM/PBSA free energy calculation method: Application to DNA conformational transitions

Journal of Computational Chemistry ◽

10.1002/jcc.21727 ◽

2011 ◽

Vol 32 (7) ◽

pp. 1431-1440 ◽

Cited By ~ 30

Author(s):

Allyn R. Brice ◽

Brian N. Dominy

Keyword(s):

Free Energy ◽

Calculation Method ◽

Conformational Transitions ◽

Free Energy Calculation ◽

Energy Calculation

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A relative free energy calculation method with ion screening effect using molecular dynamics simulation

Journal of Molecular Graphics ◽

10.1016/0263-7855(94)80025-1 ◽

1994 ◽

Vol 12 (1) ◽

pp. 56-57

Author(s):

K. Tazaki ◽

J. Doi

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Calculation Method ◽

Dynamics Simulation ◽

Free Energy Calculation ◽

Energy Calculation ◽

Screening Effect ◽

Relative Free Energy

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3H0924 On application of multi-scale ensemble modeling method to tumor suppressor p53 quaternary structure(3H Protein: Property 4,The 49th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.51.s132_5 ◽

2011 ◽

Vol 51 (supplement) ◽

pp. S132-S133

Author(s):

Tsuyoshi Terakawa ◽

Shoji Takada

Keyword(s):

Tumor Suppressor ◽

Annual Meeting ◽

Quaternary Structure ◽

Modeling Method ◽

Ensemble Modeling ◽

Tumor Suppressor P53 ◽

Multi Scale ◽

Protein Property ◽

Biophysical Society

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