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A topological description of hubs in amino Acid interaction networks.

Gaci O - Adv Bioinformatics (2010)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Le Havre University, LITIS EA 4108, BP 540, 76058 Le Havre, France.

ABSTRACT
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.

No MeSH data available.


Degree of nodes in all studied SSE-IN as a function their mean degree z. For each studied SSE-IN, we compare the degree of each node to the SSE-IN mean degree z. Less than 5% of nodes are hubs; they have a degree superior to (3/2)z.
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fig4: Degree of nodes in all studied SSE-IN as a function their mean degree z. For each studied SSE-IN, we compare the degree of each node to the SSE-IN mean degree z. Less than 5% of nodes are hubs; they have a degree superior to (3/2)z.

Mentions: In [16], we have shown that the degree distributions depend on the mean degree values. Then, we compare for each node its degree to the mean degree denoted z (see Figure 4) to illustrate how nodes interact and in particular to highlight the weak fraction of highly connected nodes, also called hubs. Further, we consider a hub as a node whose degree khub satisfies: khub > (3/2)z. The hubs represent less than 5% of the total node number; see Figure 4.


A topological description of hubs in amino Acid interaction networks.

Gaci O - Adv Bioinformatics (2010)

Degree of nodes in all studied SSE-IN as a function their mean degree z. For each studied SSE-IN, we compare the degree of each node to the SSE-IN mean degree z. Less than 5% of nodes are hubs; they have a degree superior to (3/2)z.
© Copyright Policy - open-access
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC2877201&req=5

fig4: Degree of nodes in all studied SSE-IN as a function their mean degree z. For each studied SSE-IN, we compare the degree of each node to the SSE-IN mean degree z. Less than 5% of nodes are hubs; they have a degree superior to (3/2)z.
Mentions: In [16], we have shown that the degree distributions depend on the mean degree values. Then, we compare for each node its degree to the mean degree denoted z (see Figure 4) to illustrate how nodes interact and in particular to highlight the weak fraction of highly connected nodes, also called hubs. Further, we consider a hub as a node whose degree khub satisfies: khub > (3/2)z. The hubs represent less than 5% of the total node number; see Figure 4.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Le Havre University, LITIS EA 4108, BP 540, 76058 Le Havre, France.

ABSTRACT
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.

No MeSH data available.