scholarly journals Protein Folding Simulations Combining Self-Guided Langevin Dynamics and Temperature-Based Replica Exchange

2010 ◽  
Vol 6 (8) ◽  
pp. 2477-2487 ◽  
Author(s):  
Michael S. Lee ◽  
Mark A. Olson
Keyword(s):  
Protein Folding ◽  
Langevin Dynamics ◽  
Replica Exchange ◽  
Folding Simulations

scholarly journals Deep clustering of protein folding simulations

2018 ◽  
Vol 19 (S18) ◽  
Author(s):  
Debsindhu Bhowmik ◽  
Shang Gao ◽  
Michael T. Young ◽  
Arvind Ramanathan
Keyword(s):  
Protein Folding ◽  
Folding Simulations

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).

Nonnative contact effects in protein folding

2019 ◽  
Vol 21 (22) ◽  
pp. 11924-11936 ◽  
Author(s):  
Qiang Shao ◽  
Weiliang Zhu
Keyword(s):  
Protein Folding ◽  
Folding Simulations ◽  
Structured Proteins ◽  
Contact Effects

The folding simulations of three ββα-motifs and β-barrel structured proteins (NTL9, NuG2b, and CspA) were performed to determine the important roles of native and nonnative contacts in protein folding.

scholarly journals How Robust Are Protein Folding Simulations with Respect to Force Field Parameterization?

2011 ◽  
Vol 100 (9) ◽  
pp. L47-L49 ◽  
Author(s):  
Stefano Piana ◽  
Kresten Lindorff-Larsen ◽  
David E. Shaw
Keyword(s):  
Protein Folding ◽  
Force Field ◽  
Force Field Parameterization ◽  
Folding Simulations
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