Prediction of the amino acids that have a catalytic effect on the enzymes is a major stage in appointing the activity of the enzymes and classification. The biological activity of a protein usually depends on the existence of a small number of amino acids. Recently, many algorithms have been proposed in the literature for finding these amino acids which are complex and time consuming. In this paper, we will introduce a new method for predicting the active sites that will use the spatial coordinates and the type of amino acids that contain the active sites. In order to increase the speed we use an approximate graph isomorphism algorithm. Furthermore, this algorithm allows us to find several active sites for a protein and order them according to a RMSD (Root Mean Square Deviation) number which has several applications in biology.
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