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. 2009 Oct 19;9:66. doi: 10.1186/1472-6807-9-66

Table 1.

Representations, original features, and the new features.

Repr. Original Feat. New Repr. New Feat.
SO ± 3 neighbors (± 3 NE)
Mutation (MUT)
T/pH		 SO* PAM250 (PAM)
TO Mutation (MUT)
Cα contacts (CA)
SA/T/pH		 TO* PAM250 (PAM)
Cα B-factor (BFA)
Cα B-factor (BFB)
Cα and Cβ contacts (CB)
ST ± 3 neighbors (± 3 NE)
Mutation (MUT)
Cα contacts (CA)
SA/T/pH		 ST* PAM250 (PAM)
Cα B-factor (BFA)
Cα B-factor (BFB)
Cα and Cβ contacts (CB)

In all three representations, amino acid substitution likelihood is used as a feature. B-factors of the Cα and Cβ atoms and spatial neighbor determined using both Cα and Cβ atoms are features introduced into TO and ST. The abbreviations are given only for the features that we add.