Distance matrix analysis of mutual secondary structure pairs for multiple structure alignment

The main goal of the proposed system is to enhance the mutual correlation of secondary structure element (SSE) pairs for multiple structure alignment. The algorithm utilizes the local matching advantages through distance matrix approach to extract suitable candidates of SSE pairs. The similarity scores of compared distance matrices of mutual SSE pairs were calculated and ranked to decide representative segments as key anchors for multiple structure alignment. This strategy solves the misalignment problems caused by large number of SSEs in a protein structure in previous system. In this study, the experimental results showed the hitting scores are evidently increased in those proteins which possess low sequence identity.