A novel graphical representation of proteins and its application

On the basis of three kinds of indices of physicochemical properties of twenty amino acids, a novel 3D graphical representation of protein sequences is presented. Then, the improved cumulative distance of the 3D graphical representations is defined in order to compare the proteins for similarity. Furthermore, the efficiency of our approach is illustrated by performing a comparison of similarities/dissimilarities among sequences of the ND5 proteins of nine different species. A correlation and significance analysis is provided to compare our results on similarities/dissimilarities and some other graphical representation results with the ClustalW results on similarities/dissimilarities. The comparison results show that our approach has better correlations with ClustalW for all nine species than other approaches.