Table 2 |
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Physical property terms in the GGT1 scoring function |
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| Property |
Position |
Rationale |
Explanation |
|
|
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| ARGP820103 [62] |
+3 |
Corr = 0.8(prof) |
Membrane-buried preference, lipid contact when entering binding pocket |
| LEVM760105 [69] |
+1 to +3 |
Fisher = 1.36 |
Size limitation (radius of gyration of side-chain) |
| YUTK870101 [70] |
+1 to +3 |
Fisher = 1.38 |
Hydrophobicity compensation (Unfolding Gibbs energy in water, pH7.0) |
| ZVEL_CHARG [64] |
+1 to +3 |
LS composition |
General charge penalty |
| ZVEL_CHNEG [64] |
+1 to +3 |
LS composition |
Special negative charge penalty |
| ZVEL_ALI_1 [64] |
+1 and +2 |
+2: Corr = 0.87(prof) +1: continuing deviation from Uniref50 average |
Amino-acid property: aliphatic |
| LIFS790102 [66] |
+1 and +2 |
+2: Corr = 0.77(prof) +1: continuing deviation from Uniref50 average |
Preference for extended conformations |
| FAUJ880101 [71] |
-1 and +2 |
Fisher = 1.52 |
Size, bulkiness (residues although 10 Å apart, face to same side of base pair) |
| FINA910103 [72] |
-1 |
Corr = 0.75(prof) |
Helix termination (for example, K, S favored, D,E,L,I,V disfavored) |
| KARP850103 [73] |
-7 to-1 |
-1: Corr = 0.69(prof) -2: Corr = 0.70(prof) -3: Corr = 0.71(prof) -4: Corr = 0.74(nrLS) -5: Corr = 0.75(prof) -6: Corr = 0.70(nrLS) -7: Corr = 0.78(nrLS) |
Flexibility (GGT1 lysine preference) |
| VINM940101 [67] |
-11 to -1 |
-4: Corr = 0.72(prof) -5: Corr = 0.82(prof) -6: Corr = 0.84(nrLS) -7: Corr = 0.75(nrLS) -8: Corr = 0.77(nrLS) -9: Corr = 0.68(prof) -10: Corr = 0.86(prof) Rest: continuing deviation from Uniref50 average |
Normalized flexibility average |
| KRIW790102 [68] |
-11 to -1 |
-3: Corr = 0.70(prof) -4: Corr = 0.73(prof) -5: Corr = 0.84(prof) -6: Corr = 0.81(prof) -7: Corr = 0.83(nrLS) -8: Corr = 0.85(nrLS) -9: Corr = 0.76(prof) -10: Corr = 0.86(prof) Rest: continuing deviation from Uniref50 average |
Fraction of site occupied with water |
| Buried helix (see Materials and methods) |
-20 to -1 |
Remove false positives |
Helix with strongly hydrophobic sides folds back to protein core and reduces flexibility
and accessibility of carboxy terminus |
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Maurer-Stroh and Eisenhaber Genome Biology 2005 6:R55 doi:10.1186/gb-2005-6-6-r55 |
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