scholarly journals Calculation of Protein Heat Capacity from Replica-Exchange Molecular Dynamics Simulations with Different Implicit Solvent Models

2008 ◽  
Vol 112 (47) ◽  
pp. 15064-15073 ◽  
Author(s):  
In-Chul Yeh ◽  
Michael S. Lee ◽  
Mark A. Olson
Keyword(s):  
Molecular Dynamics ◽  
Heat Capacity ◽  
Molecular Dynamics Simulations ◽  
Replica Exchange ◽  
Implicit Solvent ◽  
Replica Exchange Molecular Dynamics ◽  
Solvent Models ◽  
Dynamics Simulations ◽  
Implicit Solvent Models

Replica Exchange Molecular Dynamics Simulations of Coarse-grained Proteins in Implicit Solvent

2009 ◽  
Vol 113 (1) ◽  
pp. 267-274 ◽  
Author(s):  
Yassmine Chebaro ◽  
Xiao Dong ◽  
Rozita Laghaei ◽  
Philippe Derreumaux ◽  
Normand Mousseau
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Coarse Grained ◽  
Replica Exchange ◽  
Implicit Solvent ◽  
Replica Exchange Molecular Dynamics ◽  
Dynamics Simulations

scholarly journals Implicit solvent models fail to reproduce secondary structures of de novo designed peptides

2021 ◽  
Author(s):  
Eric Lang ◽  
Emily Baker ◽  
Derek Woolfson ◽  
Adrian Mulholland
Keyword(s):  
Molecular Dynamics ◽  
Secondary Structure ◽  
Molecular Dynamics Simulations ◽  
De Novo ◽  
Secondary Structures ◽  
Implicit Solvent ◽  
Helical Peptides ◽  
Solvent Models ◽  
Dynamics Simulations ◽  
Implicit Solvent Models

We test a range of standard implicit solvent models and protein forcefields for a set of 5 experimentally characterized, designed α-helical peptides. 65 combinations of forcefield and implicit solvent models are evaluated in >800 µs of molecular dynamics simulations. The data show that implicit solvent models generally fail to reproduce the experimentally observed secondary structure content, and none performs well for all 5 peptides. The results show that these models are not usefully predictive.

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