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Table 1 Representations, original features, and the new features.

From: Machine learning integration for predicting the effect of single amino acid substitutions on protein stability

Repr. Original Feat. New Repr. New Feat.
SO ± 3 neighbors (± 3 NE) Mutation (MUT) T/pH SO* PAM 250 (PAM)
TO Mutation (MUT) C α contacts (CA) SA/T/pH TO* PAM 250 (PAM) C α B-factor (BFA) C α B-factor (BFB) C α and C β contacts (CB)
ST ± 3 neighbors (± 3 NE) Mutation (MUT) C α contacts (CA) SA/T/pH ST* PAM 250 (PAM) C α B-factor (BFA) C α B-factor (BFB) C α and C β contacts (CB)
  1. In all three representations, amino acid substitution likelihood is used as a feature. B-factors of the C α and C β atoms and spatial neighbor determined using both C α and C β atoms are features introduced into TO and ST. The abbreviations are given only for the features that we add.