pyrexMD: Workflow-Orientated Python Package for Replica Exchange Molecular Dynamics

Python Package

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 ◽

Replica Exchange ◽

K Channel ◽

X Ray ◽

X Ray Crystallography ◽

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 ◽

Cited By ~ 50

Author(s):

Alfonso De Simone ◽

Philippe Derreumaux

Keyword(s):

Molecular Dynamics ◽

Molecular Weight ◽

Replica Exchange ◽

Low Molecular Weight ◽

Amyloid Peptides ◽

Explicit Solvent

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

Biomacromolecules ◽

10.1021/bm100646z ◽

2010 ◽

Vol 11 (12) ◽

pp. 3266-3274 ◽

Cited By ~ 22

Author(s):

Rebecca Notman ◽

E. Emre Oren ◽

Candan Tamerler ◽

Mehmet Sarikaya ◽

Ram Samudrala ◽

...

Keyword(s):

Molecular Dynamics ◽

Replica Exchange ◽

Solution Study ◽

Binding Peptides

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 ◽

Cited By ~ 33

Author(s):

In-Chul Yeh ◽

Michael S. Lee ◽

Mark A. Olson

Keyword(s):

Molecular Dynamics ◽

Heat Capacity ◽

Replica Exchange ◽

Implicit Solvent ◽

Solvent Models ◽

Dynamics Simulations ◽

Implicit Solvent Models

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 ◽

Annual Meeting ◽

Replica Exchange ◽

Biophysical Society ◽

Insights into the Folding and Unfolding Processes of Wild-Type and Mutated SH3 Domain by Molecular Dynamics and Replica Exchange Molecular Dynamics Simulations

PLoS ONE ◽

10.1371/journal.pone.0064886 ◽

2013 ◽

Vol 8 (5) ◽

pp. e64886 ◽

Cited By ~ 6

Author(s):

Wen-Ting Chu ◽

Ji-Long Zhang ◽

Qing-Chuan Zheng ◽

Lin Chen ◽

Hong-Xing Zhang

Keyword(s):

Molecular Dynamics ◽

Sh3 Domain ◽

Replica Exchange ◽

Wild Type ◽

Coarse kMC-based replica exchange algorithms for the accelerated simulation of protein folding in explicit solvent

Physical Chemistry Chemical Physics ◽

10.1039/c5cp06867c ◽

2016 ◽

Vol 18 (18) ◽

pp. 13052-13065 ◽

Cited By ~ 9

Author(s):

Emanuel K. Peter ◽

Joan-Emma Shea ◽

Igor V. Pivkin

Keyword(s):

Molecular Dynamics ◽

Monte Carlo ◽

Protein Folding ◽

Kinetic Monte Carlo ◽

Replica Exchange ◽

Accelerated Simulation ◽

Explicit Solvent ◽

Exchange Algorithms

In this paper, we present a coarse replica exchange molecular dynamics (REMD) approach, based on kinetic Monte Carlo (kMC).

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 ◽

Β Sheet

Comparison of Implicit and Explicit Solvation Models forIota-Cyclodextrin Conformation Analysis from Replica Exchange Molecular Dynamics

Journal of Chemical Information and Modeling ◽

10.1021/acs.jcim.6b00595 ◽

2017 ◽

Vol 57 (4) ◽

pp. 778-786 ◽

Cited By ~ 4

Author(s):

Wasinee Khuntawee ◽

Manaschai Kunaseth ◽

Chompoonut Rungnim ◽

Suradej Intagorn ◽

Peter Wolschann ◽

...

Keyword(s):

Molecular Dynamics ◽

Replica Exchange ◽

Conformation Analysis ◽

Solvation Models ◽

Implicit And Explicit ◽

Explicit Solvation

Effects of force fields on the conformational and dynamic properties of amyloid β(1-40) dimer explored by replica exchange molecular dynamics simulations

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.25439 ◽

2017 ◽

Vol 86 (3) ◽

pp. 279-300 ◽

Cited By ~ 13

Author(s):

Charles R. Watts ◽

Andrew Gregory ◽

Cole Frisbie ◽

Sándor Lovas

Keyword(s):

Molecular Dynamics ◽

Force Fields ◽

Dynamic Properties ◽

Amyloid Β ◽

Replica Exchange ◽