Journal of Statistical Physics. Vol. 93, Nos. 3/4, 1998, p. 673-697.
The 20 amino acid monomers composing polymeric proteins are encoded usinj their individual properties relatable to thermodynamic potentials such as aqueous partial specific volumes, aqueous molar volumes, and free energies of transfer from hydrocarbon to water solvents. These principally hydrophobic solvation, "hydrophobicity"-derived free energies are minimized in protein folding as well as protein-protein and peptide-receptor interactions. Sequential patterns in the one-dimensional distribution of these energies, reflected in dominant wavelengths of amino acid hydrophobicity, and the locations of singular hierarchical, secondary and supcrsecondary structures are elucidated by orthogonal decomposition and eigenfunction construction followed by continuous wavelet and all poles, maximum entropy power spectral transformations. The resulting graphs discriminate among examples of structural families of proteins.