title: The construction of an amino acid network for understanding protein structure and function.
abstract: Amino acid networks (AANs) are undirected networks consisting of amino acid residues and their interactions in three-dimensional protein structures. The analysis of AANs provides novel insight into protein science, and several common amino acid network properties have revealed diverse classes of proteins. In this review, we first summarize methods for the construction and characterization of AANs. We then compare software tools for the construction and analysis of AANs. Finally, we review the application of AANs for understanding protein structure and function, including the identification of functional residues, the prediction of protein folding, analyzing protein stability and protein-protein interactions, and for understanding communication within and between proteins.
authors.affiliation: Center for Systems Biology, Soochow University, Suzhou, 215006, Jiangsu, China.
authors.forename: Wenying
authors.initials: W
authors.lastname: Yan
authors.forename: Jianhong
authors.initials: J
authors.lastname: Zhou
authors.forename: Maomin
authors.initials: M
authors.lastname: Sun
authors.forename: Jiajia
authors.initials: J
authors.lastname: Chen
authors.forename: Guang
authors.initials: G
authors.lastname: Hu
authors.forename: Bairong
authors.initials: B
authors.lastname: Shen
mesh_terms: D000596:Amino Acids / Q000737:chemistry*; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods; D030562:Databases, Protein; D008958:Models, Molecular; D009211:Myoglobin / Q000737:chemistry; D011487:Protein Conformation; D017510:Protein Folding; D025941:Protein Interaction Mapping; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D040901:Proteomics / Q000379:methods; D012984:Software
chemical_list: D000596:Amino Acids; D009211:Myoglobin; D011506:Proteins