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Table 1 Physical property terms in the FT scoring function

From: Refinement and prediction of protein prenylation motifs

Property Position Rationale Explanation
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
  1. Corr, correlation; LS, learning set; nrLS, nonredundant; prof, profile.