The hydrophobic cores of proteins predicted by wavelet analysis

H. Hirakawa, S. Muta, S. Kuhara

Research output: Contribution to journalArticlepeer-review

53 Citations (Scopus)


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 (

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

All Science Journal Classification (ASJC) codes

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics


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