Table 2. Weight combinations, permutations and possible weighted sum values in the restricted grid search parameter selection scheme Weight combinationsa Number of corresponding weight permutations Nucleic Acids Research, 2008, Vol. 36, No. 4 e22 Table 3. Predicting performance of element predictors Element predictor Sensitivity Speciﬁcity Accuracy MCC PAGE 7 OF 11 1 1 115 2 þ 1153 1 115 1 þ 135 11 1 þ 15 115 4 þ 1151 1 115 1 þ 155 9 1 þ 15 135 2 þ 195 1 115 3 þ 135 9 1 þ 15 115 6 þ 195 1 115 1 þ 175 2 135 1 þ 155 7 1 þ 15 115 3 þ 155 7 1 þ 15 115 2 þ 135 7 2 þ 15 115 5 þ 135 7 1 þ 15 115 8 þ 175 1 155 3 115 2 þ 135 5 1 þ 15 115 5 þ 155 2 115 1 þ 135 5 3 þ 15 115 4 þ 135 5 2 þ 15 115 7 þ 135 5 1 þ 15 115 10 þ 155 1 135 5 115 3 þ 135 4 115 6 þ 135 3 115 9 þ 135 2 115 12 þ 135 1 115 15 Possible weighted sum values 1 1 1 1 1 1 1 2 1 1 1 15 1365 2730 15 015 2730 1365 60 060 45 045 1365 2730 60 060 90 090 270 270 45 045 455 90 090 135 135 60 060 675 675 360 360 15 015 3003 225 225 420 420 75 075 1365 1 CDK GPS KinasePhos_90 KinasePhos_95 KinasePhos_100 KinasePhos_bitscore NetPhosK_0.3 NetPhosK_0.5 NetPhosK_0.7 PPSP_highsens PPSP_balanced PPSP_highspec PredPhospho Scansite_low Scansite_medium Scansite_high CK2 GPS KinasePhos_90 KinasePhos_95 KinasePhos_100 KinasePhos_bitscore NetPhosK_0.3 NetPhosK_0.5 NetPhosK_0.7 PPSP_highsens PPSP_balanced PPSP_highspec PredPhospho Scansite_low Scansite_medium Scansite_high PKA GPS KinasePhos_90 KinasePhos_95 KinasePhos_100 KinasePhos_bitscore NetPhosK_0.3 NetPhosK_0.5 NetPhosK_0.7 PPSP_highsens PPSP_balanced PPSP_highspec PredPhospho Scansite_low Scansite_medium Scansite_high PKC GPS KinasePhos_90 KinasePhos_95 KinasePhos_100 KinasePhos_bitscore NetPhosK_0.3 NetPhosK_0.5 NetPhosK_0.7 PPSP_highsens PPSP_balanced PPSP_highspec PredPhospho Scansite_low Scansite_medium Scansite_high 0.908 0.884 0.799 0.571 0.912 1 0.639 0.065 0.983 0.905 0.054 0.898 0.667 0.405 0.153 0.699 0.581 0.476 0.266 0.594 0.961 0.755 0.245 0.930 0.742 0.048 0.594 0.576 0.380 0.135 0.817 0.722 0.650 0.361 0.775 0.878 0.694 0.483 0.967 0.850 0.008 0.808 0.644 0.422 0.158 0.718 0.649 0.480 0.129 0.687 0.716 0.491 0.333 0.954 0.741 0.006 0.598 0.411 0.170 0.069 0.800 0.717 0.837 0.923 0.685 0 0.748 0.998 0.075 0.796 0.982 0.823 0.884 0.971 0.993 0.895 0.904 0.950 0.985 0.901 0.525 0.948 1.000 0.227 0.933 1.000 0.959 0.983 0.997 1.000 0.809 0.843 0.887 0.952 0.804 0.724 0.874 0.959 0.231 0.806 0.998 0.839 0.917 0.981 0.991 0.753 0.789 0.864 0.977 0.722 0.695 0.841 0.935 0.274 0.743 1.000 0.805 0.866 0.946 0.994 0.844 0.784 0.822 0.782 0.776 0.400 0.705 0.624 0.438 0.839 0.611 0.853 0.797 0.744 0.657 0.816 0.774 0.760 0.698 0.778 0.699 0.871 0.698 0.509 0.857 0.619 0.813 0.820 0.750 0.654 0.812 0.794 0.792 0.716 0.792 0.786 0.802 0.769 0.526 0.823 0.602 0.827 0.808 0.758 0.658 0.739 0.733 0.710 0.638 0.708 0.703 0.701 0.694 0.546 0.743 0.602 0.722 0.684 0.636 0.624 0.695 0.589 0.632 0.542 0.588 N/Aa 0.387 0.188 0.128 0.687 0.100 0.708 0.571 0.479 0.290 0.613 0.523 0.504 0.386 0.530 0.506 0.730 0.403 0.208 0.700 0.171 0.616 0.640 0.512 0.293 0.618 0.569 0.560 0.405 0.573 0.590 0.583 0.525 0.270 0.645 0.048 0.642 0.596 0.515 0.288 0.466 0.441 0.378 0.211 0.404 0.403 0.358 0.348 0.289 0.477 0.059 0.412 0.315 0.189 0.179 1 2 3 4 5 6 7 8 9 0, , , , , , , , , , 15 15 15 15 15 15 15 15 15 10 11 12 13 14 , , , , 15 15 15 15 15 ,1 aWeight combinations are denoted as the sum of each weight value multiplied by the number of weights taking the weight value, with weight value 0 omitted. For instance, ‘1 1’ represents cases where one weight takes the value 1, and the other 14 weights taking the value 0; and ‘115 2 þ 1135 1’ represent cases where 2 of the 15 weights take the value 115, 1 weight takes the value 1135, and the remaining 12 weights take the value 0. Each weight combination corresponds to one or more weight permutations. For instance, for weight combination ‘1 1’, the weight value 1 can be taken by each of the 15 weights, thus it corresponds to P15 1 ¼ 15 weight permutations. Similarly, for weight combination ‘115 2 þ 1135 1’, there are P125 P113 ¼ 1365 corresponding weight permutations. slightly better predicting performance than that of the best element predictor (PredPhospho). For PKC, two combi- natorial meta-predictors achieved slightly better predicting performance than that of the best element predictor (PPSP_balanced). However, for the other two kinase families, CK2 and PKA, the combination approach did not produce meta-predictors with satisfactory predicting performances. Predicting performance assessed on MetaPS06 datasets. Element predictors having the best predicting performance are shown in italic. aMCC is undeﬁned.