Protein structure comparison using representation by line segment sequences

This paper proposes a new comparison method of tertiary protein structures. The method consists of two parts. First, a sequence of line segments which approximates each tertiary protein structure is computed. Then, an alignment of the sequences of line segments corresponding to input structures is computed. The proposed method is considered as an intermediate one between two comparison methods: a method based on topology diagram and a method based on structure alignment. Moreover it takes less CPU time than structure alignment methods because most structures are represented by means of sequences of at most 100 line segments. The effectiveness of the method is confirmed through a comparison with a previous method and an application to database searching for similar structures.