Abstract: Protein structure analysis is very important to protein function and evolution.Alignment space as a novel theory in mathematics can play a significant role in this area.This paper proposes a new index-similarity function ρ to measure the difference of proteins in 3D structure.Using the Alignment space theory and corresponding dynamic programming algorithm，the index ρ is obtained by the protein dihedral angle series.The experimental results show that the index is effective and efficient.

Key words: Alignment space, protein structure, dihedral angle series, similar measure

摘要： 蛋白质的结构分析对研究蛋白质的功能以及进化关系十分重要，而Alignment空间理论作为数学中一个崭新的方向，可以在蛋白质结构分析中发挥显著的作用。简要介绍了Alignment空间理论，采用基于蛋白质主链的二面角序列代表蛋白质的结构，利用Alignment空间理论，通过相应的动态规划算法得到了一种可以度量蛋白质结构相似程度的指标ρ。最后经由蛋白质序列的实例计算证明该指标的有效性。

关键词: Alignment空间, 蛋白质结构, 二面角序列, 相似度