The hydrophobic cores of proteins predicted by wavelet analysis

H. Hirakawa, Shigeru Muta, S. Kuhara

Research output: Contribution to journalArticle

49 Citations (Scopus)

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, prediction 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-homologus proteins can be predicted with close to 70% accuracy, without sequential alignment. Availability: The program used in this study is available from Interglactic Reality (http://www.intergalact.com).

Original languageEnglish
Pages (from-to)141-148
Number of pages8
JournalBioinformatics
Volume15
Issue number2
DOIs
Publication statusPublished - Feb 1 1999

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Wavelet Analysis
Wavelet analysis
Hydrophobicity
Alignment
Proteins
Protein
Hydrophobic and Hydrophilic Interactions
Homology
Prediction
Predict
Cross-validation
Low Frequency
Smoothing
Availability
Tend

All Science Journal Classification (ASJC) codes

  • Statistics and Probability
  • Medicine(all)
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

Cite this

The hydrophobic cores of proteins predicted by wavelet analysis. / Hirakawa, H.; Muta, Shigeru; Kuhara, S.

In: Bioinformatics, Vol. 15, No. 2, 01.02.1999, p. 141-148.

Research output: Contribution to journalArticle

Hirakawa, H. ; Muta, Shigeru ; Kuhara, S. / The hydrophobic cores of proteins predicted by wavelet analysis. In: Bioinformatics. 1999 ; Vol. 15, No. 2. pp. 141-148.
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