Figure 4.

Structural alphabet substitution matrix (SASM). The SASM is a BLOSUM-like substitution matrix for determining aligned scores for the 3D-BLAST tool, as BLOSUM matrix used in BLAST. The scores are high if the same letters (those on the main diagonal) or letters in the same category (those near the main diagonal) are aligned. In contrast, the scores are low when two letters with different properties are aligned.

Tung et al. Genome Biology 2007 8:R31   doi:10.1186/gb-2007-8-3-r31
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