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.
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Acknowledgments
We gratefully acknowledge financial support from the National Natural Science Foundation of China grants (31170795, 91230117, 91029703), the Specialized Research Fund for the Doctoral Program of Higher Education of China (20113201110015), International S&T Cooperation Program of Suzhou (SH201120) and the National High Technology Research and Development Program of China (863 program, Grant No. 2012AA02A601).
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W. Yan and J. Zhou: contributed equally to the work.
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Yan, W., Zhou, J., Sun, M. et al. The construction of an amino acid network for understanding protein structure and function. Amino Acids 46, 1419–1439 (2014). https://doi.org/10.1007/s00726-014-1710-6
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DOI: https://doi.org/10.1007/s00726-014-1710-6