Case Study on Temperature-Accelerated Molecular Dynamics Simulation of Ligand Dissociation: Inducer Dissociation from the Lac Repressor Protein

Yue Hu; Haiyan Liu

doi:10.1021/jp503856h

Case Study on Temperature-Accelerated Molecular Dynamics Simulation of Ligand Dissociation: Inducer Dissociation from the Lac Repressor Protein

The Journal of Physical Chemistry A ◽

10.1021/jp503856h ◽

2014 ◽

Vol 118 (39) ◽

pp. 9272-9279 ◽

Cited By ~ 5

Author(s):

Yue Hu ◽

Haiyan Liu

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Lac Repressor ◽

Dynamics Simulation ◽

Repressor Protein ◽

Ligand Dissociation ◽

Accelerated Molecular Dynamics

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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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Finite-size effects on the molecular dynamics simulation of fast-ion conductors: A case study of lithium garnet oxide Li7La3Zr2O12

Solid State Ionics ◽

10.1016/j.ssi.2016.03.002 ◽

2016 ◽

Vol 289 ◽

pp. 143-149 ◽

Cited By ~ 20

Author(s):

Matthew J. Klenk ◽

Wei Lai

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Size Effects ◽

Finite Size ◽

Dynamics Simulation ◽

Finite Size Effects ◽

Lithium Garnet ◽

Fast Ion Conductors ◽

Fast Ion

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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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Crystallographic structure versus homology model: a case study of molecular dynamics simulation of human and zebrafish histone deacetylase 10

Journal of Biomolecular Structure and Dynamics ◽

10.1080/07391102.2019.1691658 ◽

2019 ◽

Vol 38 (15) ◽

pp. 4397-4406 ◽

Cited By ~ 3

Author(s):

Abdullahi Ibrahim Uba ◽

Kemal Yelekçi

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Histone Deacetylase ◽

Homology Model ◽

Dynamics Simulation ◽

Crystallographic Structure ◽

Structure Versus

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Atomistic Prediction of Nanomaterials: Introduction to Molecular Dynamics Simulation and a Case Study of Graphene Wettability.

IEEE Nanotechnology Magazine ◽

10.1109/mnano.2011.2181739 ◽

2012 ◽

Vol 6 (1) ◽

pp. 8-13 ◽

Cited By ~ 4

Author(s):

Denvid Lau ◽

Raymond Lam

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Dynamics Simulation

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Nonexponential relaxation after ligand dissociation from myoglobin: a molecular dynamics simulation.

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.90.12.5805 ◽

1993 ◽

Vol 90 (12) ◽

pp. 5805-5807 ◽

Cited By ~ 45

Author(s):

K. Kuczera ◽

J. C. Lambry ◽

J. L. Martin ◽

M. Karplus

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Dynamics Simulation ◽

Ligand Dissociation

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