β-shape을 이용한 단백질 쌍의 구조정렬

Abstract

A protein is a large organic compound which plays an important role in a living cell. It is known that the similarity of two proteins implies that they share similar functions. If two proteins are similar, they are likely to have similar functions and they may have evolved from a common ancestor protein. Hence, the similarity of proteins is one of the most important issues in the molecular biology. In this paper, we present an approach to compare two proteins by aligning their structure so that their structures are maximally superposed. Structure alignment problem is to locate the correspondence pairs between two proteins, called the equivalence set, which yields the maximal superposition. Due to the computational requirement, most previous works use alpha-carbons in proteins. However, it is known that alpha-carbons do not show good performance because the alpha-carbons do not necessarily represent the appropriate shape of a protein. In this paper, we propose a new approach to a protein structure alignment based on the β-shape of the protein. Since the β-shape contains unique properties of a protein, the β-shape is more suitable for the protein structure alignment problem. Experiments show that the proposed method outperforms the previous approaches with less computation time. Key Words: structure alignment, superposition, β-shape, Voronoi