Use of information discrepancy measure to compare protein secondary structures

Protein secondary structure comparison is an important tool to explore and understand the different aspects of protein 3D structures. In this paper, transition probability matrix and structural characteristic vectors of proteins are constructed. Then the FDOD score scheme is developed to measure the similarity and the similarity tree of 20 proteins from four different classes and TOPS strings of the 36 protein chains in the Chew-Kedem dataset are constructed. The result shows that this new approach to measure the similarities between protein secondary structures is simple to implement, computationally efficient and fast.