A method of comparing protein structures based on matrix representation of secondary structure pairwise topology

This paper presents a method of comparing protein structures based on pairwise secondary structure topology. In this method, the spatial relation (sometimes rough relation) between any two secondary structural segments in a protein is represented as an element of the matrix data. The structure comparison is achieved by comparing two matrices using a pattern matching technique. In order to confirm the validity of the proposed method, experiments on similar protein retrieval was performed which showed that the method was effective.