Design of a Rotamer Library for Coarse-Grained Models in Protein-Folding Simulations

2013 ◽  
Vol 54 (1) ◽  
pp. 302-313 ◽  
Author(s):  
María Larriva ◽  
Antonio Rey
Keyword(s):  
Protein Folding ◽  
Coarse Grained ◽  
Rotamer Library ◽  
Folding Simulations

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

scholarly journals Deep clustering of protein folding simulations

2018 ◽  
Vol 19 (S18) ◽  
Author(s):  
Debsindhu Bhowmik ◽  
Shang Gao ◽  
Michael T. Young ◽  
Arvind Ramanathan
Keyword(s):  
Protein Folding ◽  
Folding Simulations

Self-Similarity of Protein Folding Flows

2012 ◽  
Vol 7 (4) ◽  
pp. 136-141
Author(s):  
I. Kalgin ◽  
Sergey Chekmarev
Keyword(s):  
Protein Folding ◽  
Sh3 Domain ◽  
Atomic Level ◽  
The Self ◽  
Coarse Grained ◽  
Folding Kinetics ◽  
Native State ◽  
Self Similarity ◽  
Folding Dynamics ◽  
Fractal Character

The problem of how a protein folds into its functional (native) state is one of the central problems of molecular biology, which attracts the attention of researchers from biology, physics and chemistry for many years. Of particular interest are general properties of the folding process, because the mechanisms of folding of different proteins can be essentially different. Previously, in the study of folding of fyn SH3 domain, we found that despite all the diversity and complexity of individual folding trajectories, the folding flows possess a well pronounced property of self-similarity, with a fractal character of the flow distributions. In the present paper, we study this phenomenon for another protein – beta3s, which is essentially different from the SH3 domain in its structure and folding kinetics. Also, in contrast to the fyn SH3 domain, for which a coarse-grained representation was used, we perform simulations on the atomic level of resolution. We show that the self-similarity and fractality of folding flows are observed is this case too, which suggests that these properties are characteristic of the protein folding dynamics

Nonnative contact effects in protein folding

2019 ◽  
Vol 21 (22) ◽  
pp. 11924-11936 ◽  
Author(s):  
Qiang Shao ◽  
Weiliang Zhu
Keyword(s):  
Protein Folding ◽  
Folding Simulations ◽  
Structured Proteins ◽  
Contact Effects

The folding simulations of three ββα-motifs and β-barrel structured proteins (NTL9, NuG2b, and CspA) were performed to determine the important roles of native and nonnative contacts in protein folding.

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