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The description of amino acids by their physico-chemical properties is open to subjective interpretation, and the numerous experimentally derived scales of hydrophobicity in the literature also differ considerably. Kanehisa and coworkers have maintained a database (AAIndex) of published amino acid indices (including hydrophobicity scales) and substitution matrices[Nakai et al., 1988,Tomii & Kanehisa, 1996, http://www.genome.ad.jp/dbget/dbget.links.html]. They also performed cluster analysis to assess the redundancy of this information in the literature. In addition to their investigation of sequence conservation (discussed above), Ladunga and Smithladunga:substitution determined which of these amino acid property indices were maximally conserved within their binary profiles. Of the non-discrete measures, the direction of the intra-side-chain hydrophobic moment calculated by Eisenberg and McLachlaneisenberg:solvation, the transfer of free energy to surface measure of Bull and Breesebull:scale, the mean polarity scale of Radzicka and Wolfendenradzicka:scale, and a number of other measures all performed better than the Kyte and Doolittle scale in their evaluation.