Minimalist Representations and the Importance of Nearest Neighbor Effects in Protein Folding Simulations

2006 ◽  
Vol 363 (4) ◽  
pp. 835-857 ◽  
Author(s):  
Andrés Colubri ◽  
Abhishek K. Jha ◽  
Min-yi Shen ◽  
Andrej Sali ◽  
R. Stephen Berry ◽  
...  
Keyword(s):  
Protein Folding ◽  
Nearest Neighbor ◽  
Neighbor Effects ◽  
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

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.

scholarly journals How Robust Are Protein Folding Simulations with Respect to Force Field Parameterization?

2011 ◽  
Vol 100 (9) ◽  
pp. L47-L49 ◽  
Author(s):  
Stefano Piana ◽  
Kresten Lindorff-Larsen ◽  
David E. Shaw
Keyword(s):  
Protein Folding ◽  
Force Field ◽  
Force Field Parameterization ◽  
Folding Simulations

scholarly journals Dynamical Analysis Methods for Protein Folding Simulations

2018 ◽  
Vol 114 (3) ◽  
pp. 45a
Author(s):  
Ayori Mitsutake ◽  
Hiroshi Takano
Keyword(s):  
Protein Folding ◽  
Dynamical Analysis ◽  
Analysis Methods ◽  
Folding Simulations
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