Table 1 |
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Physical property terms in the FT scoring function |
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| Property |
Position |
Rationale |
Explanation |
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| ARGP820103 [62] |
+3 |
Corr = 0.7(nrLS) |
Membrane-buried preference, lipid contact when entering binding pocket |
| logPREN_CKQX_FT [15] |
+3 |
Corr = -0.72(nrLS) |
Kinetic measurement, relative unprocessed FPP amounts with tetrapeptide CKQX |
| CHOC760101 [63] |
+1 to +3 |
Fisher = 1.3 |
Side chain volume |
| ZVEL_CHARG [64] |
+1 to +3 |
LS composition |
General charge penalty |
| ZVEL_CHNEG [64] |
+1 to +3 |
LS composition |
Special negative charge penalty |
| WERD780102 [65] |
+1 and +3 |
Fisher = 1.51 |
Hydrophobicity compensation for inside preference |
| ZVEL_ALI_1 [64] |
+1 and +2 |
+2: Corr = 0.85(prof) +1: continuing deviation from Uniref50 average |
Amino-acid property: aliphatic |
| LIFS790102 [66] |
+1 and +2 |
+2: Correlation = 0.76(prof) +1: continuing deviation from Uniref50 average |
Preference for extended conformations |
| ZVEL_TINY_ [64] |
-1 |
Corr = 0.68(prof) |
Size, bulkiness |
| MOBILITY_2 [21] |
-1 |
Corr = 0.61(nrLS) |
Side chain mobility |
| VINM940101 [67] |
-11 to -1 |
-2: Corr = 0.72(prof) -3: Corr = 0.75(prof) -4: Corr = 0.78(nrLS) -5: Corr = 0.82(nrLS) -6: Corr = 0.84(nrLS) -7: Corr = 0.79(nrLS) -8: Corr = 0.74(prof) -9: Corr = 0.82(nrLS) -10: Corr = 0.84(nrLS) -11: Corr = 0.79(nrLS) Rest: continuing deviation from Uniref50 average |
Normalized flexibility average |
| KRIW790102 [68] |
-11 to -1 |
-2: Corr = 0.76(prof) -6: Corr = 0.83(nrLS) -7: Corr = 0.83(nrLS) -8: Corr = 0.76(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 C-terminus |
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Corr, correlation; LS, learning set; nrLS, nonredundant; prof, profile. |
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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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