1P587 Folding free-energy landscapes of 10-residue proteins(27. Molecular dynamics simulation,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)

Daisuke Satoh; Kentaro Shimizu; Shugo Nakamura; Tohru Terada

doi:10.2142/biophys.46.s293_3

1P587 Folding free-energy landscapes of 10-residue proteins(27. Molecular dynamics simulation,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)

Seibutsu Butsuri ◽

10.2142/biophys.46.s293_3 ◽

2006 ◽

Vol 46 (supplement2) ◽

pp. S293

Author(s):

Daisuke Satoh ◽

Kentaro Shimizu ◽

Shugo Nakamura ◽

Tohru Terada

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Poster Session ◽

Dynamics Simulation ◽

Energy Landscapes ◽

Meeting Program ◽

Free Energy Landscapes ◽

Folding Free Energy

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Comment on “Deficiencies in Molecular Dynamics Simulation-Based Prediction of Protein-DNA Binding Free Energy Landscapes”

The Journal of Physical Chemistry B ◽

10.1021/acs.jpcb.8b04187 ◽

2018 ◽

Vol 124 (6) ◽

pp. 1115-1123

Author(s):

Vytautas Gapsys ◽

Morteza Khabiri ◽

Bert L. de Groot ◽

Peter L. Freddolino

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Dna Binding ◽

Binding Free Energy ◽

Dynamics Simulation ◽

Energy Landscapes ◽

Simulation Based ◽

Free Energy Landscapes

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Analysis of the Free Energy Landscapes for the Opening–Closing Dynamics of the Maltose Transporter ATPase MalK2 Using Enhanced-Sampling Molecular Dynamics Simulation

The Journal of Physical Chemistry B ◽

10.1021/acs.jpcb.5b05432 ◽

2015 ◽

Vol 119 (30) ◽

pp. 9717-9725 ◽

Cited By ~ 8

Author(s):

Wei-Lin Hsu ◽

Tadaomi Furuta ◽

Minoru Sakurai

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Dynamics Simulation ◽

Energy Landscapes ◽

Enhanced Sampling ◽

Maltose Transporter ◽

Free Energy Landscapes

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1P572 Mechanism of Ion Permeation in Model Channel; Free Energy Surface and Dynamics of K^+ Ion Transport in Anion-doped Carbon Nanotube(27. Molecular dynamics simulation,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)

Seibutsu Butsuri ◽

10.2142/biophys.46.s289_4 ◽

2006 ◽

Vol 46 (supplement2) ◽

pp. S289

Author(s):

Takashi Sumikama ◽

Shinji Saito ◽

Iwao Ohmine

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Poster Session ◽

Energy Surface ◽

Dynamics Simulation ◽

Ion Permeation ◽

Free Energy Surface ◽

Meeting Program ◽

Model Channel

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Deficiencies in Molecular Dynamics Simulation-Based Prediction of Protein–DNA Binding Free Energy Landscapes

The Journal of Physical Chemistry B ◽

10.1021/acs.jpcb.6b12450 ◽

2017 ◽

Vol 121 (20) ◽

pp. 5151-5161 ◽

Cited By ~ 11

Author(s):

Morteza Khabiri ◽

Peter L. Freddolino

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Dna Binding ◽

Binding Free Energy ◽

Dynamics Simulation ◽

Energy Landscapes ◽

Simulation Based ◽

Free Energy Landscapes

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Correction to “Deficiencies in Molecular Dynamics Simulation-Based Prediction of Protein–DNA Binding Free Energy Landscapes”

The Journal of Physical Chemistry B ◽

10.1021/acs.jpcb.0c10359 ◽

2020 ◽

Vol 124 (49) ◽

pp. 11311-11311

Author(s):

Morteza Khabiri ◽

Peter L. Freddolino

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Dna Binding ◽

Binding Free Energy ◽

Dynamics Simulation ◽

Energy Landscapes ◽

Simulation Based ◽

Free Energy Landscapes

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Free energy landscapes of small peptides in an implicit solvent model determined by force-biased multicanonical molecular dynamics simulation

Chemical Physics Letters ◽

10.1016/j.cplett.2004.10.118 ◽

2004 ◽

Vol 400 (1-3) ◽

pp. 258-263 ◽

Cited By ~ 7

Author(s):

Yukihisa S. Watanabe ◽

Jae Gil Kim ◽

Yoshifumi Fukunishi ◽

Haruki Nakamura

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Dynamics Simulation ◽

Implicit Solvent ◽

Energy Landscapes ◽

Small Peptides ◽

Implicit Solvent Model ◽

Solvent Model ◽

Free Energy Landscapes

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1P571 A Computational Study of Monoamine Oxidase A Dynamics(27. Molecular dynamics simulation,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)

Seibutsu Butsuri ◽

10.2142/biophys.46.s289_3 ◽

2006 ◽

Vol 46 (supplement2) ◽

pp. S289

Author(s):

Rossen Apostolov ◽

Yasushige Yonezawa ◽

Haruki Nakamura

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Monoamine Oxidase ◽

Poster Session ◽

Computational Study ◽

Monoamine Oxidase A ◽

Dynamics Simulation ◽

Meeting Program

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1P583 Efficient search of protein low-energy conformational space with a newly devised Wang-Landau molecular dynamics technique(27. Molecular dynamics simulation,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)

Seibutsu Butsuri ◽

10.2142/biophys.46.s292_3 ◽

2006 ◽

Vol 46 (supplement2) ◽

pp. S292

Author(s):

Takehiro Nagasima ◽

Akira R. Kinjo ◽

Takashi Mitsui ◽

Ken Nishikawa

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Poster Session ◽

Low Energy ◽

Conformational Space ◽

Dynamics Simulation ◽

Efficient Search ◽

Meeting Program

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1P280 Molecular dynamics simulation of F_0 rotary motor : rotational diffusion and proton pathway(9. Molecular motor (I),Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)

Seibutsu Butsuri ◽

10.2142/biophys.46.s216_4 ◽

2006 ◽

Vol 46 (supplement2) ◽

pp. S216

Author(s):

Hisatsugu Yamasaki ◽

Mitsunori Takano

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Poster Session ◽

Molecular Motor ◽

Rotational Diffusion ◽

Dynamics Simulation ◽

Meeting Program ◽

Rotary Motor

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2P406 Molecular Dynamics Simulation on the Glassy States of Trehalose and Neotrehalose(46. Water and bio-molecule,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)

Seibutsu Butsuri ◽

10.2142/biophys.46.s397_2 ◽

2006 ◽

Vol 46 (supplement2) ◽

pp. S397

Author(s):

Naoko Kawasaki ◽

Takao Furuki ◽

Minoru Sakurai

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Poster Session ◽

Dynamics Simulation ◽

Meeting Program

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