基于几何不变量的蛋白质三维分子结构比对  

Comparing 3-D Protein Structures Similarity by Using Geometry Invariants

作　　者：尚英姿[1] 

机构地区：[1]河北经贸大学数学与统计学院,河北石家庄050011

出　　处：《武汉大学学报（理学版）》2007年第1期37-40,共4页Journal of Wuhan University:Natural Science Edition

基　　金：国家自然科学基金(60474019);河北省自然科学基金资助项目(F2005000482)

摘　　要：为了解决蛋白质三维结构比对需要处理大量的旋转、平移变换,直接用动态规划将变得十分繁琐这一问题,在保留蛋白质空间结构属性特征的基础上,对蛋白质三维数据进行了预先的处理.通过计算蛋白质结构在旋转和平移下的几何不变量,将蛋白质的三维结构坐标变换为具有旋转、平移不变性的一维序列.进一步给出了“距离”以及“相似得分”的定义.在此基础上采用动态规划方法给出了新的蛋白质结构比对算法.对专家分类的蛋白质结构数据库进行测试,结果显示准确、快速.Sequence alignment algorithm is very mature. Smith-Waterman＇s dynamic algorithm is the most efficient and basic method in 1-dimensional sequence alignment. But it is not fit for 3-dimensional structure alignment because it requires vast time and space. In this paper, we develop a dynamic algorithm to compare two protein 3-dimensional structures by using some geometry invariants under translation and rotation. Geometry invariants include many useful features of protein 3-dimensional structure. By calculating the geometry invariants,＂distance＂ and ＂similarity scoring＂ are defined. At the end, a new algorithm based on dynamic programming is provided. Comparison with computer simulation and HOMSTRAD （HOMologous Structure Alignment Database） indicates that our approach is better in both the aligned results and alignment speed.

关 键 词：蛋白质结构 比对 相似分值 动态规划 

分 类 号：TP301.6[自动化与计算机技术—计算机系统结构]