scholarly journals CryoEM Structure Refinement by Integrating NMR Chemical Shifts with Molecular Dynamics Simulations

2017 ◽  
Vol 121 (15) ◽  
pp. 3853-3863 ◽  
Author(s):  
Juan R. Perilla ◽  
Gongpu Zhao ◽  
Manman Lu ◽  
Jiying Ning ◽  
Guangjin Hou ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Chemical Shifts ◽  
Structure Refinement ◽  
Nmr Chemical Shifts ◽  
Dynamics Simulations

Solvation chemical shifts of perylenic antenna molecules from molecular dynamics simulations

2014 ◽  
Vol 16 (40) ◽  
pp. 22309-22320 ◽  
Author(s):  
Nergiz Özcan ◽  
Jiří Mareš ◽  
Dage Sundholm ◽  
Juha Vaara
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Chemical Shifts ◽  
Solvation Model ◽  
Nmr Chemical Shifts ◽  
Dynamics Simulations ◽  
Distinct Features

Solvent-induced carbon-13 NMR chemical shifts of nine candidate antenna molecules were analysed using a dynamic solvation model, revealing the distinct features of perimeter and inside nuclear sites.

scholarly journals Using NMR Chemical Shifts as Structural Restraints in Molecular Dynamics Simulations of Proteins

Structure ◽  
2010 ◽  
Vol 18 (8) ◽  
pp. 923-933 ◽  
Author(s):  
Paul Robustelli ◽  
Kai Kohlhoff ◽  
Andrea Cavalli ◽  
Michele Vendruscolo
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Chemical Shifts ◽  
Nmr Chemical Shifts ◽  
Structural Restraints ◽  
Dynamics Simulations

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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