scholarly journals Origins of biological function in DNA and RNA hairpin loop motifs from replica exchange molecular dynamics simulation

2018 ◽  
Vol 20 (5) ◽  
pp. 2990-3001 ◽  
Author(s):  
Jacob B. Swadling ◽  
Kunihiko Ishii ◽  
Tahei Tahara ◽  
Akio Kitao
Keyword(s):  
Molecular Dynamics ◽  
Biological Function ◽  
Dynamics Simulation ◽  
Replica Exchange ◽  
Hairpin Loop ◽  
Replica Exchange Molecular Dynamics ◽  
Dna And Rna ◽  
Hairpin Loops ◽  
Rna Hairpin Loops ◽  
Rna Hairpin

Temperature REMD reveals how local chemical changes can result in markedly differing conformational landscapes for DNA and RNA hairpin loops.

scholarly journals Replica exchange molecular dynamics simulation of the coordination of Pt(ii)-Phenanthroline to amyloid-β

RSC Advances ◽  
2019 ◽  
Vol 9 (60) ◽  
pp. 35089-35097 ◽  
Author(s):  
Matthew Turner ◽  
Shaun T. Mutter ◽  
Oliver D. Kennedy-Britten ◽  
James A. Platts
Keyword(s):  
Molecular Dynamics ◽  
Tertiary Structure ◽  
Amyloid Β ◽  
Dynamics Simulation ◽  
Replica Exchange ◽  
Replica Exchange Molecular Dynamics ◽  
Metal Free ◽  
Free Peptide ◽  
Conformational Freedom ◽  
Secondary And Tertiary Structure

Replica exchange molecular dynamics are used to explore the conformational freedom of amyloid-βbound to Pt(phenanthroline), highlighting important differences in secondary and tertiary structure from the metal-free peptide.

Replica-exchange molecular dynamics simulation of diffracted X-ray tracking

2007 ◽  
Vol 33 (1-2) ◽  
pp. 97-102 ◽  
Author(s):  
Y. Kawashima ◽  
Y. C. Sasaki ◽  
Y. Sugita ◽  
T. Yoda ◽  
Y. Okamoto
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation ◽  
Replica Exchange ◽  
Replica Exchange Molecular Dynamics ◽  
X Ray

Folding of a Small RNA Hairpin Based on Simulation with Replica Exchange Molecular Dynamics

2010 ◽  
Vol 114 (17) ◽  
pp. 5835-5839 ◽  
Author(s):  
Guanghong Zuo ◽  
Wenfei Li ◽  
Jian Zhang ◽  
Jin Wang ◽  
Wei Wang
Keyword(s):  
Molecular Dynamics ◽  
Small Rna ◽  
Replica Exchange ◽  
Replica Exchange Molecular Dynamics ◽  
Rna Hairpin
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