Similarity analysis of protein sequences based on 2D and 3D amino acid adjacency matrices

This approach presents a 3D amino acid adjacency matrix based on the 2D amino acid adjacency matrix which was proposed by Randić et al. (2008) [1]. Furthermore, a novel numerical method is proposed to measure the degree of similarity based on 2D and 3D adjacency matrices. This new method is applied to nine ND5 proteins of different species. To prove the efficiency of the presented work a correlation with ClustalW and significance analyses are provided. The results show that our work is the most significant among other related works.