Influence of Ionic Aqueous Solution on the Aβ16-22 Self-Assembly: A Replica-Exchange Molecular Dynamics Study

Biophysical Journal ◽

10.1016/j.bpj.2019.11.1218 ◽

2020 ◽

Vol 118 (3) ◽

pp. 202a-203a

Author(s):

Zhenyu Qian ◽

Lili Zhu ◽

Zhiwei Liu

Keyword(s):

Molecular Dynamics ◽

Aqueous Solution ◽

Self Assembly ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

Ionic Aqueous Solution

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Structures of MERS-CoV Macro Domain in Aqueous Solution with Dynamics: Coupling Replica Exchange Molecular Dynamics and Deep Learning at the Nano Level

10.22541/au.159646074.43956314 ◽

2020 ◽

Author(s):

Ibrahim Akbayrak ◽

Burak Ulver ◽

Havvanur Dervisoglu ◽

Mehmet Haklidir ◽

Sule Caglayan ◽

...

Keyword(s):

Molecular Dynamics ◽

Aqueous Solution ◽

Deep Learning ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

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Structure of Met-enkephalin in explicit aqueous solution using replica exchange molecular dynamics

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.1167 ◽

2001 ◽

Vol 46 (2) ◽

pp. 225-234 ◽

Author(s):

K.Y. Sanbonmatsu ◽

A.E. García

Keyword(s):

Molecular Dynamics ◽

Aqueous Solution ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics

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Structural and thermodynamics characters of isolated -syn12 peptide: long-time temperature replica-exchange molecular dynamics in aqueous solution

Acta Biochimica et Biophysica Sinica ◽

10.1093/abbs/gmr002 ◽

2011 ◽

Vol 43 (3) ◽

pp. 172-180 ◽

Author(s):

Z. Cao ◽

L. Liu ◽

P. Wu ◽

J. Wang

Keyword(s):

Molecular Dynamics ◽

Aqueous Solution ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

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Replica Exchange Molecular Dynamics: A Practical Application Protocol with Solutions to Common Problems and a Peptide Aggregation and Self-Assembly Example

Methods in Molecular Biology - Peptide Self-Assembly ◽

10.1007/978-1-4939-7811-3_5 ◽

2018 ◽

pp. 101-119 ◽

Author(s):

Ruxi Qi ◽

Guanghong Wei ◽

Buyong Ma ◽

Ruth Nussinov

Keyword(s):

Molecular Dynamics ◽

Self Assembly ◽

Replica Exchange ◽

Peptide Aggregation ◽

Practical Application ◽

Replica Exchange Molecular Dynamics ◽

Common Problems

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Faculty Opinions recommendation of Mechanism of intracellular block of the KcsA K+ channel by tetrabutylammonium: insights from X-ray crystallography, electrophysiology and replica-exchange molecular dynamics simulations.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1048003.498039 ◽

2006 ◽

Author(s):

D Peter Tieleman

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Replica Exchange ◽

K Channel ◽

Replica Exchange Molecular Dynamics ◽

X Ray ◽

X Ray Crystallography ◽

Dynamics Simulations

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Molecular Dynamics Simulation and Thermodynamic Modeling of the Self-Assembly of the Triterpenoids Asiatic Acid and Madecassic Acid in Aqueous Solution

The Journal of Physical Chemistry B ◽

10.1021/jp074310g ◽

2008 ◽

Vol 112 (8) ◽

pp. 2357-2371 ◽

Author(s):

Brian C. Stephenson ◽

Arthur Goldsipe ◽

Daniel Blankschtein

Keyword(s):

Molecular Dynamics ◽

Aqueous Solution ◽

Molecular Dynamics Simulation ◽

Thermodynamic Modeling ◽

Self Assembly ◽

The Self ◽

Dynamics Simulation ◽

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Low molecular weight oligomers of amyloid peptides display β-barrel conformations: A replica exchange molecular dynamics study in explicit solvent

The Journal of Chemical Physics ◽

10.1063/1.3385470 ◽

2010 ◽

Vol 132 (16) ◽

pp. 165103 ◽

Author(s):

Alfonso De Simone ◽

Philippe Derreumaux

Keyword(s):

Molecular Dynamics ◽

Molecular Weight ◽

Replica Exchange ◽

Low Molecular Weight ◽

Amyloid Peptides ◽

Replica Exchange Molecular Dynamics ◽

Explicit Solvent

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Solution Study of Engineered Quartz Binding Peptides Using Replica Exchange Molecular Dynamics

Biomacromolecules ◽

10.1021/bm100646z ◽

2010 ◽

Vol 11 (12) ◽

pp. 3266-3274 ◽

Author(s):

Rebecca Notman ◽

E. Emre Oren ◽

Candan Tamerler ◽

Mehmet Sarikaya ◽

Ram Samudrala ◽

...

Keyword(s):

Molecular Dynamics ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

Solution Study ◽

Binding Peptides

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Calculation of Protein Heat Capacity from Replica-Exchange Molecular Dynamics Simulations with Different Implicit Solvent Models

The Journal of Physical Chemistry B ◽

10.1021/jp802469g ◽

2008 ◽

Vol 112 (47) ◽

pp. 15064-15073 ◽

Author(s):

In-Chul Yeh ◽

Michael S. Lee ◽

Mark A. Olson

Keyword(s):

Molecular Dynamics ◽

Heat Capacity ◽

Molecular Dynamics Simulations ◽

Replica Exchange ◽

Implicit Solvent ◽

Replica Exchange Molecular Dynamics ◽

Solvent Models ◽

Dynamics Simulations ◽

Implicit Solvent Models

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3P314 Conformational analysis of PA-glycans by replica-exchange molecular dynamics simulations(30.Miscellaneous topics,Poster,The 51st Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.53.s264_1 ◽

2013 ◽

Vol 53 (supplement1-2) ◽

pp. S264

Author(s):

Shigehisa Watanabe ◽

Suyong Re ◽

Eiro Muneyuki ◽

Yuji Sugita

Keyword(s):

Molecular Dynamics ◽

Conformational Analysis ◽

Molecular Dynamics Simulations ◽

Annual Meeting ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

Biophysical Society ◽

Dynamics Simulations

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