Sequence and structural features of carbohydrate binding in proteins and assessment of predictability using a neural network

Table 3 Comparison of Binary and PSSM prediction results using jackknife leave-one-out method (binding sites were labeled at 3.5 Å cut-off distance between carbohydrate and protein atoms).

Data type	Validation type	Average-sensitivity	Average-specificity	Average -net Prediction	P-value
GalBind18	Leave1 out (Using PSSM)	0.63 (0.19)	0.79 (0.09)	0.71 (0.09)	0.08859
GalBind18	Leave1 out (Using single sequences)	0.62 (0.26)	0.68 (0.12)	0.65 (0.11)
Procarb40	Leave1 out (Using PSSM)	0.87 (0.12)	0.23 (0.08)	0.55 (0.06)	0.00209
Procarb40	Leave1 out (Using single sequences)	0.68 (0.22)	0.55 (0.16)	0.61 (0.12)

Due to a large number of iterations required in a leave-one-out method, the prediction performance has a significant standard deviation, which has been shown in brackets. P-values are for two-tailed t-test conducted to distinguish between the predictions performances of single sequences versus evolutionary information coded by PSSM. In Procarb40, evolutionary profiles give a significantly poorer result than single sequences, due to a high false positive rate (low specificity).

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