通过小波分析预测的蛋白质疏水核心。

The hydrophobic cores of proteins predicted by wavelet analysis.

作者信息

Hirakawa H, Muta S, Kuhara S

机构信息

Graduate School of Genetic Resources Technology, Kyushu University, Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan.

出版信息

Bioinformatics. 1999 Feb;15(2):141-8. doi: 10.1093/bioinformatics/15.2.141.

DOI:10.1093/bioinformatics/15.2.141

PMID:10089199

Abstract

MOTIVATION

In the process of protein construction, buried hydrophobic residues tend to assemble in a core of a protein. Methods used to predict these cores involve use or no use of sequential alignment. In the case of a close homology, prediction was more accurate if sequential alignment was used. If the homology was weak, predictions would be unreliable. A hydrophobicity plot involving the hydropathy index is useful for purposes of prediction, and smoothing is essential. However, the proposed methods are insufficient. We attempted to predict hydrophobic cores with a low frequency extracted from the hydrophobicity plot, using wavelet analysis.

RESULTS

The cores were predicted at a rate of 68.7%, by cross-validation. Using wavelet analysis, the cores of non-homologous proteins can be predicted with close to 70% accuracy, without sequential alignment.

AVAILABILITY

The program used in this study is available from Intergalactic Reality (http://www.intergalact.com).

CONTACT

hirakawa@grt.kyushu-u.ac.jp, kuhara@grt.kyushu-u.ac.jp

摘要

动机

在蛋白质构建过程中，埋藏的疏水残基倾向于聚集在蛋白质的核心区域。用于预测这些核心区域的方法涉及使用或不使用序列比对。在同源性较高的情况下，如果使用序列比对，预测会更准确。如果同源性较弱，预测将不可靠。涉及亲水性指数的疏水性图谱对于预测目的很有用，并且平滑处理至关重要。然而，现有的方法并不充分。我们尝试使用小波分析从疏水性图谱中提取低频信息来预测疏水核心区域。