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Table 12 Summary of properties of structural alphabets and alphabet designs

From: Protein structure search and local structure characterization

Structural Alphabet Tung & Yang de Brevern et al. Our SA
Alphabet Size 23 16 18
How the alphabet size was determined Prespecified Iterative shrinking BIC
Clustering k-means SOM+HMM SOM+k-means
Data Set Preprocessed (Pair Database) Preprocessed (PBE-SELECT) No preprocess (nrPDB)
Substitution Matrix BLOSUM-like BLOSUM-like Self-Training
Requires known alignments to build matrix Yes Yes No
Applicability Limited Limited Modular design More flexible