The hydrophobic cores of proteins predicted by wavelet analysis

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).