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. 2004 Mar;13(3):596–607. doi: 10.1110/ps.03373104

Table 2.

The list of the features (physicochemical properties) of amino acids along with bibliographic details used in the development of cascade SVM–based methods

S.NO	Major feature	Details of features
1	Hydrophobicity	Hydrophobicity in folded form^a; hydrophobicity in unfolded form^a; hydrophobicity gain^a; surrounding hydrophobicity in α-helix^a; surrounding hydrophobicity in β-sheet^a; surrounding hydrophobicity in β-turn^a; hydrophobicity^b; average surrounding hydrophobicity^c; hydrophobicity^d
2	Hydrophilicity	Hydrophilicity^e; hydrophilicity from HPLC^f
3	Accessibility	Average accessibility surface area^g; accessibility reduction ratio^a; accessible surface area in the standard state^h; average accessible surface area in folded proteins^h
4	Flexibility	Flexibilityⁱ; local flexibility^j; flexibility for no rigid neighbors^k; flexibility for one rigid neighbor^k; flexibility for two rigid neighbors^k
5	Distribution ratio	Normalized frequency of α-helix with weights^l; normalized frequency of β-sheet with weights^l; normalized frequency for reverse turn with weights^l; percentage of buried residues^a; Percentage of exposed residues^a
6	Other features	Free energy of transfer to surface^a; polarity^a; volume^m; refractivity^d; aromatic amino acids^d; charge of amino acids^l; average number of surrounding residues^a; hydropathyⁿ

^aBull and Breese (1974)

^bEisenberg (1984)

^cManavalan and Ponnuswamy (1978)

^d J. Jones (1975)

^eHopp and Woods (1981)

^fParker et al. (1986)

^gJanin and Wodak (1978)

^hRose et al. (1985)

ⁱRagone et al. (1989)

^jBhaskaran and Ponnuswamy (1988)

^kKarplus and Schulz (1985)

^lLevitt (1978)

^mChothia (1975)

ⁿKyte and Doolittle (1982)