Intricate comparison between two given tertiary structures of proteins is as important as the comparison of their functions. Several algorithms have been devised to compute the similarity and dissimilarity among protein structures. But, these algorithms compare protein structures by structural alignment of the protein backbones which are usually unable to determine precise differences. In this paper, an attempt has been made to compute the similarities and dissimilarities among 3D protein structures using the fundamental mathematical morphology operations and fractal geometry which can resolve the problem of real differences. In doing so, two techniques are being used here in determining the superficial structural (global similarity) and local similarity in atomic level of the protein molecules. This intricate structural difference would provide insight to Biologists to understand the protein structures and their functions more precisely.
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