Sampling of near-native protein conformations during protein structure refinement using a coarse-grained model, normal modes, and molecular dynamics simulations

2007 ◽  
Vol 70 (4) ◽  
pp. 1345-1356 ◽  
Author(s):  
Andrew W. Stumpff-Kane ◽  
Katarzyna Maksimiak ◽  
Michael S. Lee ◽  
Michael Feig
Keyword(s):  
Molecular Dynamics ◽  
Protein Structure ◽  
Structure Refinement ◽  
Normal Modes ◽  
Coarse Grained ◽  
Protein Conformations ◽  
Native Protein ◽  
Coarse Grained Model ◽  
Protein Structure Refinement ◽  
Dynamics Simulations

scholarly journals A Generic Force Field for Simulating Native Protein Structures Using Dissipative Particle Dynamics

Soft Matter ◽  
2021 ◽  
Author(s):  
Rakesh K Vaiwala ◽  
Ganapathy Ayappa
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Dissipative Particle Dynamics ◽  
Protein Structures ◽  
Particle Dynamics ◽  
Coarse Grained ◽  
Native Protein ◽  
Dynamics Simulations

A coarse-grained force field for molecular dynamics simulations of native structures of proteins in a dissipative particle dynamics (DPD) framework is developed. The parameters for bonded interactions are derived by...

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