Comparative analysis of protein primary sequences with graph energy

Haiyan Wu, Yusen Zhang, Wei Chen and Zengchao Mu

Physica A: Statistical Mechanics and its Applications, 2015, vol. 437, issue C, 249-262

Abstract: We propose in this paper, the graph energy and Laplacian energy of 20 amino acids based on the codons coding the amino acids and apply them to put forward a novel 2-D graphical representation of proteins. The novel graphical representation has no circuit or degeneracy, uniquely represents proteins and allows one to easily and quickly visually observe and inspect similarity/dissimilarity between them. It also leads to two novel protein descriptors, the graph energy of a protein sequence, and the increment of graph energy between two protein sequences. We develop similarities/dissimilarities model and successfully analyze the similarities/dissimilarities of ND5, 36PDs, 24TFs and 27AFPs with good results consistent with ClustalW even better ones.

Keywords: The graph energy; Laplacian energy; 2-D graphical representation; The increment of graphical energy; Similarity (search for similar items in EconPapers)
Date: 2015
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Persistent link: https://EconPapers.repec.org/RePEc:eee:phsmap:v:437:y:2015:i:c:p:249-262

DOI: 10.1016/j.physa.2015.04.017

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