Initial Binding of Ions to the Interhelical Loops of Divalent Ion Transporter CorA: Replica Exchange Molecular Dynamics Simulation Study

PLoS ONE ◽

10.1371/journal.pone.0043872 ◽

2012 ◽

Vol 7 (8) ◽

pp. e43872 ◽

Author(s):

Tong Zhang ◽

Yuguang Mu

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Simulation Study ◽

Dynamics Simulation ◽

Replica Exchange ◽

Ion Transporter ◽

Replica Exchange Molecular Dynamics ◽

Initial Binding

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On the Structural Stability of a Short Three Stranded β-sheet Peptide (Betanova): Replica Exchange Molecular Dynamics Simulation Study

Bulletin of the Korean Chemical Society ◽

10.5012/bkcs.2010.31.8.2386 ◽

2010 ◽

Vol 31 (8) ◽

pp. 2386-2388

Author(s):

Soon-Min Jang ◽

Eun-Ae Kim ◽

Young-Shang Pak

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Structural Stability ◽

Simulation Study ◽

Dynamics Simulation ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

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Reversible Temperature and Pressure Denaturation of a Protein Fragment: A Replica Exchange Molecular Dynamics Simulation Study

Physical Review Letters ◽

10.1103/physrevlett.93.238105 ◽

2004 ◽

Vol 93 (23) ◽

Author(s):

Dietmar Paschek ◽

Angel E. García

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Simulation Study ◽

Dynamics Simulation ◽

Replica Exchange ◽

Protein Fragment ◽

Replica Exchange Molecular Dynamics ◽

Temperature And Pressure

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Replica exchange molecular dynamics simulation study on the mechanism of desiccation-induced structuralization of an intrinsically disordered peptide as a model of LEA proteins

Biophysics and Physicobiology ◽

10.2142/biophysico.16.0_196 ◽

2019 ◽

Vol 16 (0) ◽

pp. 196-204 ◽

Author(s):

Tatsushi Nishimoto ◽

Yuta Takahashi ◽

Shohei Miyama ◽

Tadaomi Furuta ◽

Minoru Sakurai

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Simulation Study ◽

Dynamics Simulation ◽

Replica Exchange ◽

Lea Proteins ◽

Replica Exchange Molecular Dynamics ◽

Intrinsically Disordered ◽

Intrinsically Disordered Peptide

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Effects of the fixed end in single-molecule imaging techniques: A replica-exchange molecular dynamics simulation study

Chemical Physics Letters ◽

10.1016/j.cplett.2005.07.120 ◽

2005 ◽

Vol 414 (4-6) ◽

pp. 449-455 ◽

Author(s):

Y. Kawashima ◽

Y. Sugita ◽

T. Yoda ◽

Y. Okamoto

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Single Molecule ◽

Simulation Study ◽

Imaging Techniques ◽

Dynamics Simulation ◽

Replica Exchange ◽

Single Molecule Imaging ◽

Replica Exchange Molecular Dynamics ◽

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Temperature-mediated switching of protectant-denaturant behavior of trimethylamine-N-oxide and consequences on protein stability from a replica exchange molecular dynamics simulation study

Molecular Simulation ◽

10.1080/08927022.2016.1233546 ◽

2016 ◽

Vol 43 (1) ◽

pp. 52-64 ◽

Author(s):

Gargi Borgohain ◽

Sandip Paul

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Protein Stability ◽

Simulation Study ◽

Dynamics Simulation ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics

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Phase Behavior of a Lipid Bilayer System Studied by a Replica-Exchange Molecular Dynamics Simulation

Journal of the Physical Society of Japan ◽

10.1143/jpsj.81.024002 ◽

2012 ◽

Vol 81 (2) ◽

pp. 024002 ◽

Author(s):

Tetsuro Nagai ◽

Ryuichi Ueoka ◽

Yuko Okamoto

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Phase Behavior ◽

Lipid Bilayer ◽

Dynamics Simulation ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

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In silico study of osmolytic effects of choline-O-sulfate on urea induced unfolding of Trp-cage mini-protein: An atomistic view from replica exchange molecular dynamics simulation

Archives of Biochemistry and Biophysics ◽

10.1016/j.abb.2020.108484 ◽

2020 ◽

Vol 695 ◽

pp. 108484

Author(s):

Srijita Paul ◽

Sandip Paul

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

In Silico ◽

Dynamics Simulation ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

In Silico Study

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Replica-exchange molecular dynamics simulation of diffracted X-ray tracking

Molecular Simulation ◽

10.1080/08927020601067581 ◽

2007 ◽

Vol 33 (1-2) ◽

pp. 97-102 ◽

Author(s):

Y. Kawashima ◽

Y. C. Sasaki ◽

Y. Sugita ◽

T. Yoda ◽

Y. Okamoto

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Dynamics Simulation ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

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Transformation of a design peptide between the α-helix and β-hairpin structures using a helix-strand replica-exchange molecular dynamics simulation

Physical Chemistry Chemical Physics ◽

10.1039/c3cp44443k ◽

2013 ◽

Vol 15 (33) ◽

pp. 13852 ◽

Author(s):

Hisashi Okumura ◽

Satoru G. Itoh

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Dynamics Simulation ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

Hairpin Structures ◽

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Structural Diversity and Changes in Conformational Equilibria of Biantennary Complex-Type N-Glycans in Water Revealed by Replica-Exchange Molecular Dynamics Simulation

Biophysical Journal ◽

10.1016/j.bpj.2011.10.019 ◽

2011 ◽

Vol 101 (10) ◽

pp. L44-L46 ◽

Author(s):

Suyong Re ◽

Naoyuki Miyashita ◽

Yoshiki Yamaguchi ◽

Yuji Sugita

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Structural Diversity ◽

Dynamics Simulation ◽

Replica Exchange ◽

Complex Type ◽

Replica Exchange Molecular Dynamics ◽

Conformational Equilibria

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