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Table 6 The mean MCC and BDT raw scores and Z-scores obtained by FunFOLD are compared with those obtained by the top CASP9 function prediction groups for the partial binding sites analysis.

From: FunFOLD: an improved automated method for the prediction of ligand binding residues using 3D models of proteins

Group ID N Mean score for group Mean score for FunFOLD Difference in mean score Mean Z-score for group Mean Z-score for FunFOLD P-value
(raw score)
P-value
(Z-score)
1 - p-value
(raw score)
1 - p-value
(Z-score)
   MCC BDT MCC BDT MCC BDT MCC BDT MCC BDT MCC BDT MCC BDT MCC BDT MCC BDT
FN096 24 0.626 0.520 0.508 0.439 -0.188 -0.018 0.526 0.413 0.052 0.108 0.954 0.879 0.938 0.853 0.004 0.049 0.062 0.049
FN035 20 0.636 0.545 0.531 0.467 -0.105 -0.078 0.512 0.593 0.095 0.144 0.897 0.951 0.904 0.951 0.103 0.131 0.096 0.241
FN339 24 0.597 0.492 0.508 0.439 -0.089 -0.053 0.458 0.333 0.052 0.108 0.932 0.772 0.897 0.815 0.068 0.121 0.103 0.147
FN242 23 0.591 0.505 0.504 0.439 -0.087 -0.066 0.457 0.404 0.023 0.101 0.948 0.767 0.952 0.817 0.052 0.233 0.048 0.183
FN104 22 0.619 0.538 0.513 0.447 -0.106 -0.091 0.366 0.350 0.004 0.043 0.973 0.962 0.968 0.912 0.027 0.038 0.032 0.088
FN315 21 0.620 0.459 0.538 0.439 -0.081 -0.020 0.332 0.152 0.085 0.108 0.784 0.698 0.671 0.637 0.216 0.228 0.329 0.185
FN110 22 0.594 0.548 0.546 0.470 -0.048 -0.078 0.233 0.430 0.133 0.161 0.487 0.869 0.375 0.759 0.513 0.277 0.625 0.364
FN094 23 0.552 0.482 0.531 0.458 -0.021 -0.024 0.171 0.177 0.129 0.168 0.596 0.723 0.537 0.636 0.404 0.302 0.463 0.363
FN114 23 0.548 0.479 0.499 0.436 -0.049 -0.044 0.063 0.014 0.005 0.055 0.745 0.723 0.555 0.458 0.255 0.277 0.445 0.542
FN452 22 0.543 0.448 0.518 0.451 -0.025 0.003 0.011 -0.082 0.023 0.091 0.588 0.334 0.524 0.257 0.412 0.666 0.476 0.743
FN236 24 0.486 0.418 0.508 0.439 0.022 0.021 -0.049 -0.147 0.052 0.108 0.440 0.361 0.404 0.269 0.596 0.639 0.596 0.731
FN425 23 0.409 0.346 0.507 0.439 0.097 0.093 -0.323 -0.349 0.035 0.111 0.111 0.031 0.111 0.054 0.886 0.969 0.889 0.946
FN017 23 0.403 0.376 0.531 0.458 0.128 0.094 -0.501 -0.397 0.129 0.168 0.019 0.016 0.013 0.011 0.981 0.941 0.987 0.951
FN057 23 0.424 0.364 0.531 0.458 0.107 0.082 -0.534 -0.373 0.129 0.168 0.026 0.059 0.013 0.049 0.974 0.984 0.987 0.989
FN113 22 0.477 0.381 0.523 0.456 0.046 0.075 -0.548 -0.594 0.082 0.114 0.126 0.049 0.044 0.035 0.874 0.972 0.956 0.984
FN072 23 0.418 0.366 0.531 0.458 0.113 0.092 -0.551 -0.446 0.129 0.168 0.019 0.028 0.012 0.016 0.981 0.991 0.988 0.996
FN415 23 0.388 0.353 0.531 0.458 0.142 0.105 -0.619 -0.542 0.129 0.168 0.007 0.009 0.006 0.004 0.993 0.951 0.994 0.975
  1. The analysis is based on common subsets of all CASP9 targets, with a minimum of 10 predictions in common. N, size of the common subset used in the comparison; MCC, Matthews Correlation Coefficient; BDT, the Binding Site Distance Test Score [36].P-value, the p-value for the paired Wilcoxon signed rank sum test using the raw scores; P-value (Z-score), the p-value for the paired Wilcoxon signed rank sum test using the Z-scores; 1 - p-value, 1 minus the p-value for the paired Wilcoxon signed rank sum test using the raw scores; 1-p-value (Z-score), 1 minus the p-value for the paired Wilcoxon signed rank sum test using the Z-scores. The table is sorted by the Mean MCC Z-score for groups with the best CASP9 groups at the top. The highest mean scores, mean Z-scores, significant p-values and significant 1-p-values are indicated in bold. Server groups are underlined.