Accelerated Molecular Dynamics Simulation for Helical Proteins Folding in Explicit Water

Frontiers in Chemistry ◽

10.3389/fchem.2019.00540 ◽

2019 ◽

Vol 7 ◽

Cited By ~ 11

Author(s):

Lili Duan ◽

Xiaona Guo ◽

Yalong Cong ◽

Guoqiang Feng ◽

Yuchen Li ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Dynamics Simulation ◽

Accelerated Molecular Dynamics ◽

Helical Proteins ◽

Explicit Water

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Accelerated molecular dynamics simulation using multi-core CPU and GPU

Journal of Computer Applications ◽

10.3724/sp.j.1087.2011.00843 ◽

2011 ◽

Vol 31 (3) ◽

pp. 843-847

Author(s):

Jiang-hong LIN ◽

Jin-xian LIN ◽

Tun LU

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Dynamics Simulation ◽

Accelerated Molecular Dynamics

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GPU-Accelerated Molecular Dynamics Simulation to Study Liquid Crystal Phase Transition Using Coarse-Grained Gay-Berne Anisotropic Potential

PLoS ONE ◽

10.1371/journal.pone.0151704 ◽

2016 ◽

Vol 11 (3) ◽

pp. e0151704 ◽

Cited By ~ 5

Author(s):

Wenduo Chen ◽

Youliang Zhu ◽

Fengchao Cui ◽

Lunyang Liu ◽

Zhaoyan Sun ◽

...

Keyword(s):

Phase Transition ◽

Molecular Dynamics ◽

Liquid Crystal ◽

Molecular Dynamics Simulation ◽

Dynamics Simulation ◽

Coarse Grained ◽

Liquid Crystal Phase ◽

Accelerated Molecular Dynamics ◽

Crystal Phase Transition ◽

Liquid Crystal Phase Transition

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Accelerated molecular dynamics simulation of the thermal desorption of n-alkanes from the basal plane of graphite

The Journal of Chemical Physics ◽

10.1063/1.2364894 ◽

2006 ◽

Vol 125 (18) ◽

pp. 184706 ◽

Cited By ~ 38

Author(s):

Kelly E. Becker ◽

Kristen A. Fichthorn

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Thermal Desorption ◽

Basal Plane ◽

Dynamics Simulation ◽

Accelerated Molecular Dynamics

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Temperature-accelerated molecular dynamics simulation of the evolution of a low-energy incident Cu3 cluster on the Cu(100) surface with a monoatomic step

Journal of Surface Investigation X-ray Synchrotron and Neutron Techniques ◽

10.1134/s1027451016030216 ◽

2016 ◽

Vol 10 (3) ◽

pp. 570-575 ◽

Cited By ~ 2

Author(s):

E. V. Duda ◽

G. V. Kornich

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Low Energy ◽

Dynamics Simulation ◽

Accelerated Molecular Dynamics ◽

Energy Incident

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3P243 Analysis of the photoresponse mechanism of the LOV-HTH system using accelerated molecular dynamics simulation(Photobiology: Vision & Photoreception,Poster,The 52th Annual Meeting of the Biophysical Society of Japan(BSJ2014))

Seibutsu Butsuri ◽

10.2142/biophys.54.s289_3 ◽

2014 ◽

Vol 54 (supplement1-2) ◽

pp. S289

Author(s):

Kokubu Tetsuo ◽

Furuta Tadaomi ◽

Sakurai Minoru

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Annual Meeting ◽

Dynamics Simulation ◽

Accelerated Molecular Dynamics ◽

Biophysical Society

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Accelerated Molecular-Dynamics Simulation of Thin Film Growth

Springer Proceedings in Physics - Computer Simulation Studies in Condensed-Matter Physics XIX ◽

10.1007/978-3-540-85625-2_2 ◽

2008 ◽

pp. 7-16 ◽

Cited By ~ 2

Author(s):

K. A. Fichthorn ◽

R. A. Miron

Keyword(s):

Thin Film ◽

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Film Growth ◽

Thin Film Growth ◽

Dynamics Simulation ◽

Accelerated Molecular Dynamics

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Molecular dynamics simulation of C8E5micelle in explicit water: structure and hydrophobic solvation thermodynamics

Molecular Physics ◽

10.1080/00268970110118312 ◽

2002 ◽

Vol 100 (14) ◽

pp. 2299-2306 ◽

Cited By ~ 37

Author(s):

SHEKHAR GARDE ◽

LU YANG ◽

JONATHAN S. DORDICK ◽

MICHAEL E. PAULAITIS

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Water Structure ◽

Dynamics Simulation ◽

Solvation Thermodynamics ◽

Hydrophobic Solvation ◽

Explicit Water

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How Does Agonist and Antagonist Binding Lead to Different Conformational Ensemble Equilibria of the κ-Opioid Receptor: Insight from Long-Time Gaussian Accelerated Molecular Dynamics Simulation

ACS Chemical Neuroscience ◽

10.1021/acschemneuro.8b00535 ◽

2018 ◽

Vol 10 (3) ◽

pp. 1575-1584 ◽

Cited By ~ 3

Author(s):

Xiaoli An ◽

Qifeng Bai ◽

Zhitong Bing ◽

Shuangyan Zhou ◽

Danfeng Shi ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Opioid Receptor ◽

Dynamics Simulation ◽

Conformational Ensemble ◽

Accelerated Molecular Dynamics ◽

Long Time ◽

Agonist And Antagonist ◽

Antagonist Binding

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Effect of pH on the Aggregation of α-syn12 Dimer in Explicit Water by Replica-Exchange Molecular Dynamics Simulation

International Journal of Molecular Sciences ◽

10.3390/ijms160714291 ◽

2015 ◽

Vol 16 (12) ◽

pp. 14291-14304 ◽

Cited By ~ 1

Author(s):

Zanxia Cao ◽

Xiumei Zhang ◽

Lei Liu ◽

Liling Zhao ◽

Haiyan Li ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Dynamics Simulation ◽

Replica Exchange ◽

Effect Of Ph ◽

Replica Exchange Molecular Dynamics ◽

Explicit Water

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Charactering Amyloid-Beta Protein Misfolding from Molecular Dynamics Simulation with Explicit Water

Biophysical Journal ◽

10.1016/j.bpj.2009.12.3559 ◽

2010 ◽

Vol 98 (3) ◽

pp. 649a

Author(s):

Chewook Lee ◽

Sihyun Ham

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Amyloid Beta ◽

Protein Misfolding ◽

Dynamics Simulation ◽

Amyloid Beta Protein ◽

Explicit Water

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