A novel and effective scoring scheme for structure classification and pairwise similarity measurement

Protein tertiary structure defines its functions, classification and binding sites. Similar structural characteristics between two proteins often lead to the similar characteristics thereof. Determining structural similarity accurately in real time is a crucial research issue. In this paper, we present a novel and effective scoring scheme that is dependent on novel features extracted from protein alpha carbon distance matrices. Our scoring scheme is inspired from pattern recognition and computer vision. Our method is significantly better than the current state of the art methods in terms of family match of pairs of protein structures and other statistical measurements. The effectiveness of our method is tested on standard benchmark structures. A web service is available at http://research.buet.ac.bd:8080/Comograd/score.html where you can get the similarity measurement score between two protein structures based on our method. Keywords—Pairwise protein structure comparison, scoring function, structural similarity