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

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.

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

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

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

2016 ◽  
Vol 18 (18) ◽  
pp. 13052-13065 ◽  
Author(s):  
Emanuel K. Peter ◽  
Joan-Emma Shea ◽  
Igor V. Pivkin
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo ◽  
Protein Folding ◽  
Kinetic Monte Carlo ◽  
Replica Exchange ◽  
Replica Exchange Molecular Dynamics ◽  
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).

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