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Chemical similarity scoring

The aim with chemical similarity scoring schemes is to give greater weight to the alignment of amino acids with similar physico-chemical properties. This is desirable since major changes in amino acid type could reduce the ability of the protein to perform its biological role and hence the protein would be selected against during the course of evolution. The intuitive scheme developed by McLachlan [6] classified amino acids on the basis of polar or non-polar character, size, shape and charge and gives a score of 6 to interconversions between identical rare amino acids (eg F, F) reducing to 0 for substitutions between amino acids of quite different character (eg. F, E). Feng et al. [3] encode features similar to McLachlan by combining information from the structural features of the amino acids and the redundancy of the genetic code.