In this paper we introduce the notion of protein interaction network. This is a graph whose vertices are the protein's amino acids and whose edges are the interactions between them. Using a graph theory approach, we identify a number of properties of these networks. We compare them to the general small-world network model and we analyze their hierarchical structure.
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.
In this paper, we present a means to fold amino acid interaction networks. This is a graph whose vertices are the proteins amino acids and whose edges are the interactions between them. Our approach consists in exploiting the parallel between topological and structural properties. Thus, we establish a relation between the sequence and the structure relying on topological criteria. To fold this type of graph, we limit the topological space and we exploit an ant colony approach. We consider those graphs as dynamic graphs so that we can observe gradually the graph properties during the folding process.
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