Classification of zinc hydrolases using a structure-based phylogenetic method / Nurul Atikah Mohd Sany

Computational method of structural alignment is a method that had managed to grasp the attention of many people in the research world. Compared to the sequence alignment method, structural alignment method can bring people closer to the functions of proteins as the proteins structure are closely related to its function. SCOP databases had been used as a standard databases in order to obtain information about structural classification. However, problem rises as the SCOP database is developed manually and the computational method that is on par with this method has not been developed yet. The problem in this research is to determine whether the computational method is comparable to the SCOP classification. The objectives of this research is to assess the similarities of zinc hydrolases based on phylogenetic method, to construct phylogenetic tree by using similarity values from protein alignment and validate phylogenetic tree against standard protein classification. The result obtained show that structural alignment managed to produce tree with higher cluster order compared to the sequence alignment tree. When compared to Wouters et al. (2001 ),result obtained is almost similar and with increment of sample size, problems found in Wouters et al. managed to be solved in this research. Then it can be concluded that the structural alignment is a great method to be use in producing an accurate phylogenetic tree, conducting multiple structural alignment and identifying function of unknown proteins. However this method is not really accurate in classifying proteins with high sequence identity.