scholarly journals Biophysical and computational methods to analyze amino acid interaction networks in proteins

2016 ◽  
Vol 14 ◽  
pp. 245-251 ◽  
Author(s):  
Kathleen F. O'Rourke ◽  
Scott D. Gorman ◽  
David D. Boehr
Keyword(s):  
Amino Acid ◽  
Computational Methods ◽  
Interaction Networks ◽  
Acid Interaction ◽  
Amino Acid Interaction ◽  
Analyze Amino Acid

scholarly journals A Topological Description of Hubs in Amino Acid Interaction Networks

2010 ◽  
Vol 2010 ◽  
pp. 1-9 ◽  
Author(s):  
Omar Gaci
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Interaction Networks ◽  
Acid Interaction ◽  
Scale Free ◽  
Topological Description ◽  
General Rules ◽  
Scale Free Networks ◽  
Amino Acid Interaction ◽  
Folded Proteins

We represent proteins by amino acid interaction networks. This is a graph whose vertices are the proteins amino acids and whose edges are the interactions between them. Once we have compared this type of graphs to the general model of scale-free networks, we analyze the existence of nodes which highly interact, the hubs. We describe these nodes taking into account their position in the primary structure to study their apparition frequency in the folded proteins. Finally, we observe that their interaction level is a consequence of the general rules which govern the folding process.

scholarly journals Millisecond Timescale Motions Connect Amino Acid Interaction Networks in Alpha Tryptophan Synthase

2018 ◽  
Vol 5 ◽  
Author(s):  
Kathleen F. O'Rourke ◽  
Jennifer M. Axe ◽  
Rebecca N. D'Amico ◽  
Debashish Sahu ◽  
David D. Boehr
Keyword(s):  
Amino Acid ◽  
Interaction Networks ◽  
Tryptophan Synthase ◽  
Acid Interaction ◽  
Amino Acid Interaction
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