scholarly journals A Novel Approach of Dynamic Cross Correlation Analysis on Molecular Dynamics Simulations and Its Application to Ets1 Dimer–DNA Complex

PLoS ONE ◽  
2014 ◽  
Vol 9 (11) ◽  
pp. e112419 ◽  
Author(s):  
Kota Kasahara ◽  
Ikuo Fukuda ◽  
Haruki Nakamura
Keyword(s):  
Molecular Dynamics ◽  
Correlation Analysis ◽  
Molecular Dynamics Simulations ◽  
Cross Correlation ◽  
Novel Approach ◽  
Cross Correlation Analysis ◽  
Dynamics Simulations ◽  
Dna Complex

scholarly journals Combining enhanced sampling with experiment-directed simulation of the GYG peptide

2018 ◽  
Vol 17 (03) ◽  
pp. 1840007 ◽  
Author(s):  
Dilnoza B. Amirkulova ◽  
Andrew D. White
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Chemical Shifts ◽  
Parallel Tempering ◽  
Collective Variables ◽  
Novel Approach ◽  
Sampling Problem ◽  
Combination Of Methods ◽  
Dynamics Simulations ◽  
Explicit Water

Experiment-directed simulation (EDS) is a technique to minimally bias molecular dynamics simulations to match experimentally observed results. The method improves accuracy but does not address the sampling problem of molecular dynamics simulations of large systems. This work combines EDS with both the parallel-tempering or parallel-tempering well-tempered ensemble replica-exchange methods to enhance sampling. These methods are demonstrated on the GYG tripeptide in explicit water. The collective variables biased by EDS are chemical shifts, where the set-points are determined by NMR experiments. The results show that it is possible to enhance sampling with either parallel-tempering and parallel-tempering well-tempered ensemble in the EDS method. This combination of methods provides a novel approach for both accurately and exhaustively simulating biological systems.

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