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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.


Cumulative degree distribution for 1COY SSE-IN. The curve decreases quickly for degrees superior to the mean degree z which acts as a threshold.
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fig3: Cumulative degree distribution for 1COY SSE-IN. The curve decreases quickly for degrees superior to the mean degree z which acts as a threshold.

Mentions: As well, we have shown that the mean degree values constitute a threshold for protein SSE-IN cumulative degree distribution. For degrees lower than z, the cumulative distribution decreases slowly and after this threshold its decrease is fast compared to an exponential one; see Figure 3.


A topological description of hubs in amino Acid interaction networks.

Gaci O - Adv Bioinformatics (2010)

Cumulative degree distribution for 1COY SSE-IN. The curve decreases quickly for degrees superior to the mean degree z which acts as a threshold.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2877201&req=5

fig3: Cumulative degree distribution for 1COY SSE-IN. The curve decreases quickly for degrees superior to the mean degree z which acts as a threshold.
Mentions: As well, we have shown that the mean degree values constitute a threshold for protein SSE-IN cumulative degree distribution. For degrees lower than z, the cumulative distribution decreases slowly and after this threshold its decrease is fast compared to an exponential one; see Figure 3.

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.