Exploring the energy landscape of protein folding using replica-exchange and conventional molecular dynamics simulations

David A.C. Beck; George W.N. White; Valerie Daggett

doi:10.1016/j.jsb.2006.10.002

Exploring the energy landscape of protein folding using replica-exchange and conventional molecular dynamics simulations

Journal of Structural Biology ◽

10.1016/j.jsb.2006.10.002 ◽

2007 ◽

Vol 157 (3) ◽

pp. 514-523 ◽

Cited By ~ 43

Author(s):

David A.C. Beck ◽

George W.N. White ◽

Valerie Daggett

Keyword(s):

Molecular Dynamics ◽

Protein Folding ◽

Molecular Dynamics Simulations ◽

Energy Landscape ◽

Replica Exchange ◽

Dynamics Simulations

Download Full-text

Replica-exchange molecular dynamics simulations for a small-sized protein folding with implicit solvent

Journal of Molecular Structure THEOCHEM ◽

10.1016/s0166-1280(03)00371-3 ◽

2003 ◽

Vol 634 (1-3) ◽

pp. 235-241 ◽

Cited By ~ 21

Author(s):

A. Suenaga

Keyword(s):

Molecular Dynamics ◽

Protein Folding ◽

Molecular Dynamics Simulations ◽

Replica Exchange ◽

Implicit Solvent ◽

Replica Exchange Molecular Dynamics ◽

Dynamics Simulations

Download Full-text

Faculty Opinions recommendation of Experimental resolution of early steps in protein folding: testing molecular dynamics simulations.

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

10.3410/f.1019474.220524 ◽

2004 ◽

Author(s):

Angel García

Keyword(s):

Molecular Dynamics ◽

Protein Folding ◽

Molecular Dynamics Simulations ◽

Experimental Resolution ◽

Dynamics Simulations

Download Full-text

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

Download Full-text

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 ◽

Molecular Dynamics Simulations ◽

Replica Exchange ◽

Implicit Solvent ◽

Replica Exchange Molecular Dynamics ◽

Solvent Models ◽

Dynamics Simulations ◽

Implicit Solvent Models

Download Full-text

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

Download Full-text

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 ◽

Molecular Dynamics Simulations ◽

Sh3 Domain ◽

Replica Exchange ◽

Wild Type ◽

Replica Exchange Molecular Dynamics ◽

Dynamics Simulations

Download Full-text

Probing Protein Folding Landscape by Using Combined Force Spectroscopy and Molecular Dynamics Simulations

Biophysical Journal ◽

10.1016/j.bpj.2017.11.2284 ◽

2018 ◽

Vol 114 (3) ◽

pp. 412a

Author(s):

Ha H. Truong ◽

Susan Marqusee

Keyword(s):

Molecular Dynamics ◽

Protein Folding ◽

Molecular Dynamics Simulations ◽

Force Spectroscopy ◽

Dynamics Simulations

Download Full-text

Describing Protein Folding Kinetics by Molecular Dynamics Simulations. 1. Theory†

The Journal of Physical Chemistry B ◽

10.1021/jp037421y ◽

2004 ◽

Vol 108 (21) ◽

pp. 6571-6581 ◽

Cited By ~ 287

Author(s):

William C. Swope ◽

Jed W. Pitera ◽

Frank Suits

Keyword(s):

Molecular Dynamics ◽

Protein Folding ◽

Molecular Dynamics Simulations ◽

Folding Kinetics ◽

Dynamics Simulations

Download Full-text

Protein folding: Molecular dynamics simulations and in vitro studies for probing mechanism of urea- and guanidinium chloride-induced unfolding of horse cytochrome-c

International Journal of Biological Macromolecules ◽

10.1016/j.ijbiomac.2018.10.186 ◽

2019 ◽

Vol 122 ◽

pp. 695-704 ◽

Cited By ~ 8

Author(s):

Sabab Hasan Khan ◽

Amresh Prakash ◽

Preeti Pandey ◽

Andrew M. Lynn ◽

Asimul Islam ◽

...

Keyword(s):

Molecular Dynamics ◽

Protein Folding ◽

Cytochrome C ◽

Molecular Dynamics Simulations ◽

In Vitro Studies ◽

Guanidinium Chloride ◽

Dynamics Simulations ◽

Horse Cytochrome

Download Full-text

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 ◽

Molecular Dynamics Simulations ◽

Force Fields ◽

Dynamic Properties ◽

Amyloid Β ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

Dynamics Simulations

Download Full-text