Molecular Dynamics for Simulating the Protein Folding Process Using the 3D AB Off-Lattice Model

2012 ◽  
pp. 61-72 ◽  
Author(s):  
César Manuel Vargas Benítez ◽  
Heitor Silvério Lopes
Keyword(s):  
Molecular Dynamics ◽  
Protein Folding ◽  
Lattice Model ◽  
Folding Process

Ab-Initio Protein Folding Using Molecular Dynamics and a Simplified Off-Lattice Model

2013 ◽  
Vol 7 (4) ◽  
pp. 391-402 ◽  
Author(s):  
CésarM. V. Benítez ◽  
Heitor Silvério Lopes
Keyword(s):  
Molecular Dynamics ◽  
Protein Folding ◽  
Ab Initio ◽  
Lattice Model

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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