scholarly journals A replica exchange Monte Carlo algorithm for protein folding in the HP model

2007 ◽  
Vol 8 (1) ◽  
pp. 342 ◽  
Author(s):  
Chris Thachuk ◽  
Alena Shmygelska ◽  
Holger H Hoos
Keyword(s):  
Monte Carlo ◽  
Protein Folding ◽  
Monte Carlo Algorithm ◽  
Replica Exchange ◽  
Hp Model ◽  
Replica Exchange Monte Carlo

Massive replica exchange Monte Carlo algorithm: a tool to access high pressure thermodynamics of hard systems

2018 ◽  
Vol 20 (43) ◽  
pp. 27490-27500 ◽  
Author(s):  
Eduardo Basurto ◽  
Catalina Haro-Pérez ◽  
Carlos A. Vargas ◽  
Gerardo Odriozola
Keyword(s):  
High Pressure ◽  
Monte Carlo ◽  
High Pressures ◽  
Monte Carlo Algorithm ◽  
Replica Exchange ◽  
Circular Cavity ◽  
Optimal Packing ◽  
Replica Exchange Monte Carlo

Pressure increases with the replica index, so that the size of the circular cavity decreases. Hence, the system is ordered by the replica index. At high pressures an optimal packing is produced.

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).

scholarly journals In Silico Generation of Peptides by Replica Exchange Monte Carlo: Docking-Based Optimization of Maltose-Binding-Protein Ligands

PLoS ONE ◽  
2015 ◽  
Vol 10 (8) ◽  
pp. e0133571 ◽  
Author(s):  
Anna Russo ◽  
Pasqualina Liana Scognamiglio ◽  
Rolando Pablo Hong Enriquez ◽  
Carlo Santambrogio ◽  
Rita Grandori ◽  
...  
Keyword(s):  
Monte Carlo ◽  
In Silico ◽  
Binding Protein ◽  
Maltose Binding Protein ◽  
Replica Exchange ◽  
Protein Ligands ◽  
Replica Exchange Monte Carlo
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