Protein folding simulations: From coarse-grained model to all-atom model

IUBMB Life ◽  
2009 ◽  
Vol 61 (6) ◽  
pp. 627-643 ◽  
Author(s):  
Jian Zhang ◽  
Wenfei Li ◽  
Jun Wang ◽  
Meng Qin ◽  
Lei Wu ◽  
...  
Keyword(s):  
Protein Folding ◽  
Coarse Grained ◽  
Coarse Grained Model ◽  
Atom Model ◽  
Folding Simulations

PathMolD-AB: Spatiotemporal pathways of protein folding using parallel molecular dynamics with a coarse-grained model

2020 ◽  
Vol 87 ◽  
pp. 107301
Author(s):  
Leandro Takeshi Hattori ◽  
Bruna Araujo Pinheiro ◽  
Rafael Bertolini Frigori ◽  
César Manuel Vargas Benítez ◽  
Heitor Silvério Lopes
Keyword(s):  
Molecular Dynamics ◽  
Protein Folding ◽  
Coarse Grained ◽  
Coarse Grained Model ◽  
Parallel Molecular Dynamics

Coarse-grained model for protein folding based on structural profiles

2011 ◽  
Vol 84 (4) ◽  
Author(s):  
Katrin Wolff ◽  
Michele Vendruscolo ◽  
Markus Porto
Keyword(s):  
Protein Folding ◽  
Coarse Grained ◽  
Coarse Grained Model

How Concentration and Crowding Impact Protein Stability: Insights From a Coarse-Grained Model

2008 ◽  
Author(s):  
Thomas M. Truskett
Keyword(s):  
Protein Folding ◽  
Protein Stability ◽  
Molecular Species ◽  
Current Understanding ◽  
Coarse Grained ◽  
Heterogeneous Environments ◽  
Native State ◽  
Coarse Grained Model ◽  
High Concentrations ◽  
The Stability

Much of the current understanding of the protein folding problem derives from studies of proteins in dilute solutions. However, in many systems of scientific and engineering interest, proteins must fold in concentrated, heterogeneous environments. Cells are crowded with many molecular species, and chaperones often sequester proteins and promote rapid folding. Proteins are also present in high concentrations in the manufacture, storage, and delivery of biotherapeutics. How does crowding generally affect the stability of the native state? Are all crowding agents created equal? If not, can generic structural or chemical features forecast their effects on protein stability?

scholarly journals Generic Coarse-Grained Model for Protein Folding and Aggregation

2009 ◽  
Vol 96 (3) ◽  
pp. 405a ◽  
Author(s):  
Tristan Bereau ◽  
Markus Deserno
Keyword(s):  
Protein Folding ◽  
Coarse Grained ◽  
Coarse Grained Model

scholarly journals Generic coarse-grained model for protein folding and aggregation

2009 ◽  
Vol 130 (23) ◽  
pp. 235106 ◽  
Author(s):  
Tristan Bereau ◽  
Markus Deserno
Keyword(s):  
Protein Folding ◽  
Coarse Grained ◽  
Coarse Grained Model
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