PCPMer (Physical Chemical Property Based Motif Analyzer ) is a software package for determining conserved regions in multiple sequence alignments. The software represents each of the 20 naturally occuring amino acids by five quantitative descriptors and can detect motifs (short regions of significant conservation) in aligned sequences based on relative entropy or physicochemical similarity. It can be then used to search for related proteins in a protein sequence database and map the variability data on a 3D structure (to make a stereophysicochemical variability plot, or SVP). Such plots are particularly useful for identifying the spatial relationships of highly conserved or variable residues to one another.
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Schein, C.H., Zhou, B. and Braun, W.
Stereophysicochemical variability plots highlight conserved antigenic areas in Flaviviruses.
Virol. J. Apr 21;2(1):40, 2005