Folding of Fourteen Small Proteins with a Residue-Specific Force Field and Replica-Exchange Molecular Dynamics

2014 ◽  
Vol 136 (27) ◽  
pp. 9536-9539 ◽  
Author(s):  
Fan Jiang ◽  
Yun-Dong Wu
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Replica Exchange ◽  
Specific Force ◽  
Replica Exchange Molecular Dynamics ◽  
Small Proteins

scholarly journals Application of Multiplexed Replica Exchange Molecular Dynamics to the UNRES Force Field: Tests with α and α+β Proteins

2009 ◽  
Vol 5 (3) ◽  
pp. 627-640 ◽  
Author(s):  
Cezary Czaplewski ◽  
Sebastian Kalinowski ◽  
Adam Liwo ◽  
Harold A. Scheraga
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Field Tests ◽  
Replica Exchange ◽  
Replica Exchange Molecular Dynamics

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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