Toward an Enhanced Sampling Molecular Dynamics Method for Studying Ligand-Induced Conformational Changes in Proteins

The Journal of Physical Chemistry B ◽

10.1021/acs.jpcb.5b07816 ◽

2015 ◽

Vol 119 (46) ◽

pp. 14594-14603 ◽

Author(s):

Ole Juul Andersen ◽

Julie Grouleff ◽

Perri Needham ◽

Ross C. Walker ◽

Frank Jensen

Keyword(s):

Molecular Dynamics ◽

Conformational Changes ◽

Molecular Dynamics Method ◽

Enhanced Sampling ◽

Dynamics Method

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Surface-Tension Replica-Exchange Molecular Dynamics Method for Enhanced Sampling of Biological Membrane Systems

Journal of Chemical Theory and Computation ◽

10.1021/ct400445k ◽

2013 ◽

Vol 9 (12) ◽

pp. 5629-5640 ◽

Author(s):

Takaharu Mori ◽

Jaewoon Jung ◽

Yuji Sugita

Keyword(s):

Molecular Dynamics ◽

Surface Tension ◽

Biological Membrane ◽

Molecular Dynamics Method ◽

Replica Exchange ◽

Enhanced Sampling ◽

Membrane Systems ◽

Replica Exchange Molecular Dynamics ◽

Dynamics Method

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Linear Response Path Following: A Molecular Dynamics Method To Simulate Global Conformational Changes of Protein upon Ligand Binding

Journal of Chemical Theory and Computation ◽

10.1021/acs.jctc.5b00120 ◽

2015 ◽

Vol 11 (7) ◽

pp. 2900-2917 ◽

Author(s):

Koichi Tamura ◽

Shigehiko Hayashi

Keyword(s):

Molecular Dynamics ◽

Ligand Binding ◽

Conformational Changes ◽

Linear Response ◽

Path Following ◽

Molecular Dynamics Method ◽

Dynamics Method

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Nanoparticle thermal diffusion simulation in dense gases and fluids by the molecular dynamics method

Оптика атмосферы и океана ◽

10.15372/aoo20160610 ◽

2016 ◽

Vol 29 (6) ◽

Keyword(s):

Molecular Dynamics ◽

Thermal Diffusion ◽

Molecular Dynamics Method ◽

Dense Gases ◽

Diffusion Simulation ◽

Dynamics Method

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Study on Interactive Multi-resolution Molecular Dynamics Method

Journal of the Visualization Society of Japan ◽

10.3154/jvs.20.1supplement_43 ◽

2000 ◽

Vol 20 (1Supplement) ◽

pp. 43-46

Author(s):

Ken-ichi SAITOH ◽

Takashi DOI ◽

Masao KOMAYA ◽

Takehiko INABA

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Method ◽

Dynamics Method

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Modeling Nano-Metric Manufacturing Processes with Molecular Dynamics Method: A Review

Current Nanoscience ◽

10.2174/1573413712666160530122851 ◽

2016 ◽

Vol 13 (1) ◽

pp. 3-20 ◽

Author(s):

Nikolaos E. Karkalos ◽

Angelos P. Markopoulos

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Method ◽

Manufacturing Processes ◽

Dynamics Method

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Structural evolution of aluminum hydride nanoparticles in water using ReaxFF molecular dynamics method

Materials Today Communications ◽

10.1016/j.mtcomm.2020.101804 ◽

2020 ◽

pp. 101804 ◽

Author(s):

Liang Song ◽

Feng-Qi Zhao ◽

Si-Yu Xu ◽

Cai-Chao Ye ◽

Xue-Hai Ju

Keyword(s):

Molecular Dynamics ◽

Aluminum Hydride ◽

Structural Evolution ◽

Molecular Dynamics Method ◽

Dynamics Method

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Two-phase solid/liquid mixture of water/carbon nanotubes at the equilibration phase of atomic structures: Atomic value effects in a microchannel using the Molecular Dynamics method

Journal of Molecular Liquids ◽

10.1016/j.molliq.2021.116820 ◽

2021 ◽

pp. 116820

Author(s):

Mostafa Naderi ◽

Arash Karimipour

Keyword(s):

Carbon Nanotubes ◽

Molecular Dynamics ◽

Liquid Mixture ◽

Molecular Dynamics Method ◽

Two Phase ◽

Atomic Structures ◽

Solid Liquid ◽

Dynamics Method

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A computational study of mixed-mode crack growth: Molecular dynamics method

10.1063/5.0036664 ◽

2020 ◽

Author(s):

L. V. Stepanova ◽

O. N. Belova

Keyword(s):

Molecular Dynamics ◽

Crack Growth ◽

Computational Study ◽

Molecular Dynamics Method ◽

Mixed Mode Crack ◽

Dynamics Method

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Computer simulation of a two-dimensional ideal gas: a simple molecular dynamics method for teaching purposes

European Journal of Physics ◽

10.1088/0143-0807/6/3/005 ◽

1985 ◽

Vol 6 (3) ◽

pp. 148-153 ◽

Author(s):

M L Aiello-Nicosia ◽

R M Sperandeo-Mineo

Keyword(s):

Molecular Dynamics ◽

Computer Simulation ◽

Ideal Gas ◽

Molecular Dynamics Method ◽

Two Dimensional ◽

Dynamics Method

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Composition effect on thermophobicity of ternary mixtures: An enhanced molecular dynamics method

The Journal of Chemical Physics ◽

10.1063/1.5031004 ◽

2018 ◽

Vol 149 (3) ◽

pp. 034502

Author(s):

Sylvie Antoun ◽

M. Ziad Saghir ◽

S. Srinivasan

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Method ◽

Ternary Mixtures ◽

Composition Effect ◽

Dynamics Method

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