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Table 1 List of the AAIndex indices used in this paper

From: An improved sequence based prediction protocol for DNA-binding proteins using SVM and comprehensive feature analysis

Feature ID AAIndex ID Feature description
39 CHOP780202 Normalized frequency of beta-sheet (Chou-Fasman, 1978b)
56 CIDH920103 Normalized hydrophobicity scales for alpha+beta-proteins (Cid et al., 1992)
58 CIDH920105 Normalized average hydrophobicity scales (Cid et al., 1992)
86 FAUJ880109 Number of hydrogen bond donors (Fauchere et al., 1988)
88 FAUJ880111 Positive charge (Fauchere et al., 1988)
95 FINA910104 Helix termination parameter at posision j+1 (Finkelstein et al., 1991)
100 GEIM800104 Alpha-helix indices for alpha/beta-proteins (Geisow-Roberts, 1980)
102 GEIM800106 Beta-strand indices for beta-proteins (Geisow-Roberts, 1980)
139 KANM800102 Average relative probability of beta-sheet (Kanehisa-Tsong, 1980)
146 KLEP840101 Net charge (Klein et al., 1984)
147 KRIW710101 Side chain interaction parameter (Krigbaum-Rubin, 1971)
167 LIFS790101 Conformational preference for all beta-strands (Lifson-Sander, 1979)
178 MEEJ800101 Retention coefficient in HPLC, pH7.4 (Meek, 1980)
214 OOBM770102 Short and medium range non-bonded energy per atom (Oobatake-Ooi, 1977)
229 PALJ810107 Normalized frequency of alpha-helix in all-alpha class (Palau et al., 1981)
280 QIAN880123 Weights for beta-sheet at the window position of 3 (Qian-Sejnowski, 1988)
299 RACS770103 Side chain orientational preference (Rackovsky-Scheraga, 1977)
321 RADA880108 Mean polarity (Radzicka-Wolfenden, 1988)
356 ROSM880102 Side chain hydropathy, corrected for solvation (Roseman, 1988)
365 SWER830101 Optimal matching hydrophobicity (Sweet-Eisenberg, 1983)
399 ZIMJ680102 Bulkiness (Zimmerman et al., 1968)
401 ZIMJ680104 Isoelectric point (Zimmerman et al., 1968)
422 AURR980120 Normalized positional residue frequency at helix termini C4’ (Aurora-Rose, 1998)
431 MUNV940103 Free energy in beta-strand conformation (Munoz-Serrano, 1994)
449 NADH010104 Hydropathy scale based on self-information values in the two-state model (20% accessibility) (Naderi-Manesh et al., 2001)
451 NADH010106 Hydropathy scale based on self-information values in the two-state model (36% accessibility) (Naderi-Manesh et al., 2001)
512 GUYH850105 Apparent partition energies calculated from Chothia index (Guy, 1985)
528 MIYS990104 Optimized relative partition energies - method C (Miyazawa-Jernigan, 1999)
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BMC Bioinformatics

ISSN: 1471-2105

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