Table 6 |
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Physicochemical properties used by the FEATURE algorithm |
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Atom-based |
Molecule-based |
Residue-based |
Secondary structure-based |
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ATOM-TYPE-IS-C |
PARTIAL-CHARGE |
RESIDUE_NAME_IS_ALA |
SECONDARY_STRUCTURE1_IS_3HELIX |
|
ATOM-TYPE-IS-CT |
HYDROXYL |
RESIDUE_NAME_IS_ARG |
SECONDARY_STRUCTURE1_IS_4HELIX |
|
ATOM-TYPE-IS-Ca |
AMIDE |
RESIDUE_NAME_IS_ASN |
SECONDARY_STRUCTURE1_IS_5HELIX |
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ATOM-TYPE-IS-N |
AMINE |
RESIDUE_NAME_IS_ASP |
SECONDARY_STRUCTURE1_IS_BRIDGE |
|
ATOM-TYPE-IS-N2 |
CARBONYL |
RESIDUE_NAME_IS_CYS |
SECONDARY_STRUCTURE1_IS_STRAND |
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ATOM-TYPE-IS-N3 |
RING-SYSTEM |
RESIDUE_NAME_IS_GLN |
SECONDARY_STRUCTURE1_IS_TURN |
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ATOM-TYPE-IS-Na |
PEPTIDE |
RESIDUE_NAME_IS_GLU |
SECONDARY_STRUCTURE1_IS_BEND |
|
ATOM-TYPE-IS-O |
VDW-VOLUME |
RESIDUE_NAME_IS_GLY |
SECONDARY_STRUCTURE1_IS_COIL |
|
ATOM-TYPE-IS-O2 |
CHARGE |
RESIDUE_NAME_IS_HIS |
SECONDARY_STRUCTURE1_IS_HET |
|
ATOM-TYPE-IS-OH |
NEG-CHARGE |
RESIDUE_NAME_IS_ILE |
SECONDARY_STRUCTURE1_IS_UNKNOWN |
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ATOM-TYPE-IS-S |
POS-CHARGE |
RESIDUE_NAME_IS_LEU |
SECONDARY_STRUCTURE1_IS_HELIX |
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ATOM-TYPE-IS-SH |
CHARGE-WITH-HIS |
RESIDUE_NAME_IS_LYS |
SECONDARY_STRUCTURE1_IS_BETA |
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ATOM-TYPE-IS-OTHER |
HYDROPHOBICITY |
RESIDUE_NAME_IS_MET |
SECONDARY_STRUCTURE1_IS_COIL |
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ATOM-NAME-IS-ANY |
MOBILITY |
RESIDUE_NAME_IS_PHE |
SECONDARY_STRUCTURE1_IS_HET |
|
ATOM-NAME-IS-C |
SOLVENT-ACCESSIBILITY |
RESIDUE_NAME_IS_PRO |
SECONDARY_STRUCTURE1_IS_UNKNOWN |
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ATOM-NAME-IS-N |
RESIDUE_NAME_IS_SER |
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ATOM-NAME-IS-O |
RESIDUE_NAME_IS_THR |
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ATOM-NAME-IS-S |
RESIDUE_NAME_IS_TRP |
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ATOM-NAME-IS-OTHER |
RESIDUE_NAME_IS_TYR |
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RESIDUE_NAME_IS_VAL |
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RESIDUE_NAME_IS_HOH |
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RESIDUE_NAME_IS_OTHER |
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CLASS1_IS_HYDROPHOBIC |
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CLASS1_IS_CHARGED |
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CLASS1_IS_POLAR |
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CLASS1_IS_UNKNOWN |
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CLASS2_IS_NONPOLAR |
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CLASS2_IS_POLAR |
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CLASS2_IS_BASIC |
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CLASS2_IS_ACIDIC |
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CLASS2_IS_UNKNOWN |
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These properties are expressed at the atomic, molecular, residue and secondary structural levels of abstraction. The properties at the atomic, molecule and secondary structural level are designed to make the FEATURE models relatively less dependent on primary amino acid sequence, in an attempt to improve performance on highly divergent (or convergent) sites. Most of these properties are simply counts of the property, and a few are continuous valued, as discussed in [32]. |
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Wu et al. Genome Biology 2008 9:R8 doi:10.1186/gb-2008-9-1-r8 |
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