A Study of Protein Structure using Amino Acid Interaction Networks
Résumé
In this chapter we represent proteins by amino acid interaction networks. The nodes in these networks correspond to amino acids. Two nodes are linked if the distance between the corresponding amino acids in the folded protein is below a certain threshold. Ignoring details, such as the type and the exact position of each amino acid, this abstract and compact description allows to focus on the interactions' structure and organization. Interaction networks for proteins of known structure can be easily obtained using the information available in Protein Data Bank. We study amino acid interaction networks using graph theory tools in order to determine their main characteristics, such as mean degree, degree distribution, mean node distances, etc. Some of these characteristics are common to all proteins while others are different for different classes of proteins.
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