Classification and Feature Extraction of Protein Structures Based on Structural Transformation

This paper presents a new method of comparison of protein structures from the viewpoint of the secondary structural elements. The structural similarity can be evaluated through the structure transformation from one protein to the other, which is composed of a set of predefined primitive operations that are applied to each of the secondary structural elements. The cost that is required for each of the primitive operations is defined in advance, and the similarity between the proteins is calculated as the total cost of transformation that is the sum of costs for applied primitive operations. In addition, a feature extraction method that is also based on the structural transformation is presented. In this method, the feature to be extracted is defined as a pair including a representative structure and a cluster region. The representative structure is generated by estimating the center of structural balance among proteins in one cluster using the transformation costs. The cluster region shows how far the cluster has spread. The effectiveness of these methods are empirically demonstrated through the experiments using the data in the Brookhaven Protein Data Bank.