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基于离散小波变换的膜蛋白跨膜螺旋区段预测

于 彬1，王广彬1，王翼飞2   

  1. 1. 青岛科技大学 数理学院, 山东 青岛 266061;

    2. 上海大学 理学院, 上海 200444

  • 收稿日期:2007-05-15 修回日期:2007-08-08 出版日期:2008-01-31 发布日期:2008-01-31

Prediction of Transmembrane Helical Segments in Membrane Proteins Based on Discrete Wavelet Transform

YU Bin1 , WANG Guang-bin1, WANG Yi-fei2   

  1. 1. College of Mathematics and Physics, Qingdao University of Science and Technology, Qingdao 266061, China;

    2. College of Science, Shanghai University, Shanghai 200444, China

  • Received:2007-05-15 Revised:2007-08-08 Online:2008-01-31 Published:2008-01-31

被引次数

1

摘要： 基因组计划所产生的大量蛋白质序列迫切需要从理论上预测跨膜螺旋区段。文中采用基于离散小波变换的方法预测膜蛋白跨膜螺旋区段的数目和位置。以PDB 代码为1KQG的膜蛋白为例，描述了该方法对跨膜螺旋区段的数目和位置的预测分析过程。从最新的MPtopo数据库中随机抽取80条三维结构已知的膜蛋白序列作为测试集 (含325个跨膜螺旋区)，采用该方法对跨膜螺旋区段进行预测，其中312个跨膜螺旋区被准确预测到，预测准确率为96.6%。并将预测结果与7种常用预测方法的主要预测结果进行了比较。结果表明，本文提出的方法具有较高的预测准确度。

关键词: 离散小波变换, 膜蛋白, 跨膜螺旋区段, 疏水性

Abstract: Increasing protein sequences from the genome project require theoretical methods to predict transmembrane helical segments (TMHs). In this paper, a method based on discrete wavelet transform (DWT) is developed to predict the number and location of TMHs in membrane proteins. PDB coded as 1KQG is chosen as an example to describe the prediction process with this method. Eighty proteins with known 3D-structure from the Mptopo database are chosen at random as the test objects (including 325 TMHs), 312 of which can be predicted and the prediction accuracy is 96.6%. Compared with main prediction results of seven common prediction methods, the obtained results indicate that the proposed method has higher prediction accuracy.

Key words: discrete wavelet transform, membrane protein, transmembrane helical segments, hydrophobicity