aminoacid similarity matrices

 I am trying to find all the available aminoacid scoring matrices that
 are used for analyzing protein sequences (eg for phylogenetic analysis,
 sequence alignment, homology modeling etc). So far, I got my hands
 on the Dayhoff matrix (many versions of it) which measures the evolu-
 tionary distance between the aminoacids. I know people have constructed
 similarity matrices based on physicochemical properties, tertiary
 structure alignments etc, but I can't locate them on the web. Your
 help would be greatly appreciated.
 Dimitris K. Agrafiotis, PhD              | e-mail: dimitris { *at * }
 Senior Fellow                            | tel:    (610) 458-6045
 3-Dimensional Pharmaceuticals, Inc.      | fax:    (610) 458-8249
 665 Stockton Drive, Suite 104
 Exton, PA 19341