  In this paper, we develop a quantitative comparison method for two arbitrary
protein structures. This method uses a root-mean-square deviation (RMSD)
characterization and employs a series expansion of the protein's shape function
in terms of the Wigner-D functions to define a new criterion, which is called a
"similarity value". We further demonstrate that the expansion coefficients for
the shape function obtained with the help of the Wigner-D functions correspond
to structure factors. Our method addresses the common problem of comparing two
proteins with different numbers of atoms. We illustrate it with a worked
example.
