Protein structure classification by structural transformation

Protein structure classification plays an important role in understanding the relationships among structure and sequence. Recently, as the number of known protein structure are increasing steeply, automatic classification is highly required. This paper presents a new method of classification of protein folds based on the structural similarities between a pair of proteins from the viewpoint of the secondary structural elements. The similarity can be evaluated through the structural transformation from one protein to the other, which is composed of a set of predefined primitive operations. Since the similarity is scored with the total cost of the transformation, the method requires no threshold value. The effectiveness of the method was empirically demonstrated through the experiments using the data in the Brookhaven Protein Data Bank.