EMPSC: A New Method Based on Ellipsoidal Model for Protein Structure Comparison

This paper proposes a new method EMPSC for the well-known PSC (Protein Structure Comparison) problem. The proposed method EMPSC is a protein structural alignment algorithm based on ellipsoidal model abstraction. We segment the protein 3D structure into two different kinds of structures, including Secondary Structure Elements recognized by DSSP and other coil/loop structures. These SSEs will be the initial alignment center for obtaining the transformation coordinate systems. Different heuristic filters and geometric hashing based global alignment estimation are used for quick finding better initial alignments. In the refined alignment stage of analysis, a standard refinement algorithm is invoked to fine-tune the alignment outputted by the first stage. Our experimental results reveal that EMPSC generally achieves comparable accuracy and better performance in comparison with the existing PSC algorithms. Moreover, we analyzed the factors that affect the EMPSC performance and SSE-based PSC algorithms. Further investigation in multiple protein structure comparison and local structure comparison will be continued.