BioInformatics Lecture Notes

                                   Amino Acid Substitution Matrices (continued)

Other similarity scoring matrices might be constructed from any property of amino acids that can be quantified -partition coefficients between hydrophobic and hydrophilic phases
-molecular volume, etc.

Unfortunately, all these biophysical quantities suffer from the fact that they provide only a partial view of the picture - there is no guarantee, that any particular property  is a good predictor for conservation of amino acids between related proteins.