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The hydrophobic cores of proteins predicted by wavelet analysis
1Graduate School of Genetic Resources Technology, Kyushu University, Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan.
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