  By using a mixture model for the density distribution of the three pseudobond
angles formed by $C_\alpha$ atoms of four consecutive residues, the local
structural states are discretized as 17 conformational letters of a protein
structural alphabet. This coarse-graining procedure converts a 3D structure to
a 1D code sequence. A substitution matrix between these letters is constructed
based on the structural alignments of the FSSP database.
