#Results from Pucci Sym dataset*
KORPM_Pucci2018N.txt Full dataset KORPM_Pucci2018dirN.txt Direct subset KORPM_Pucci2018revN.txt Reverse subset *_prc.txt Corresponding PRC Curves
Equivalent result files for Cartddg, FoldX, Evo, PopMs, Dynamut, DDGun3D, ACDCNN methods
#Comparative TABLES
S D T TP avg err FP TN avg err FN P N SEN SPE PPV NPV ACC accn RMSE MAE PCC Sc Ob1 Ob2 MCC AUC_R AUC_P THROC Sen Spe BMCC TH Sen Spe
KORPM 342 342 684 264 1.4 0.9 72 270 -1.5 0.9 78 336 348 0.772 0.789 0.786 0.776 0.781 0.781 1.332 0.951 0.690 65.9 33.6 0.4 0.56 0.860 0.857 -0.022 0.781 0.784 0.574 -0.164 0.845 0.725
KORPM* 342 342 684 264 1.5 0.9 71 271 -1.5 0.8 78 335 349 0.772 0.792 0.788 0.777 0.782 0.782 1.331 0.969 0.695 64.6 34.6 0.7 0.56 0.860 0.853 -0.153 0.827 0.749 0.578 -0.153 0.827 0.749
Cartddg 342 342 684 198 1.4 1.6 42 300 -1.4 2.9 144 240 444 0.579 0.877 0.825 0.676 0.728 0.728 3.438 2.633 0.633 52.3 41.1 6.6 0.48 0.812 0.818 -0.879 0.716 0.787 0.504 -0.879 0.716 0.787
FoldX 342 342 684 188 1.4 0.8 77 265 -1.5 1.0 154 265 419 0.550 0.775 0.709 0.632 0.662 0.662 1.862 1.286 0.537 60.1 34.5 5.4 0.33 0.737 0.749 -0.231 0.629 0.711 0.370 0.178 0.518 0.833
Evo 342 342 684 209 1.4 0.8 102 240 -1.5 0.9 133 311 373 0.611 0.702 0.672 0.643 0.656 0.656 1.562 1.123 0.543 61.7 34.9 3.4 0.31 0.742 0.754 -0.106 0.681 0.675 0.359 0.277 0.520 0.822
PopMs 342 342 684 229 1.4 1.0 100 242 -1.5 1.1 113 329 355 0.670 0.708 0.696 0.682 0.689 0.689 1.581 1.147 0.521 56.6 42.4 1.0 0.38 0.754 0.734 0.001 0.670 0.708 0.386 0.247 0.497 0.863
Dynamut2 342 342 684 72 1.5 1.2 40 302 -1.4 0.8 270 112 572 0.211 0.883 0.643 0.528 0.547 0.547 1.879 1.368 0.380 54.4 38.2 7.5 0.13 0.623 0.616 -0.690 0.626 0.526 0.238 -1.848 0.944 0.219
DDGun3D 342 342 684 233 1.4 0.9 105 237 -1.4 0.9 109 338 346 0.681 0.693 0.689 0.685 0.687 0.687 1.434 1.039 0.627 61.8 37.4 0.7 0.37 0.751 0.755 0.027 0.637 0.725 0.364 0.027 0.637 0.725
TherNet 342 342 684 223 1.5 1.0 102 240 -1.5 1.0 119 325 359 0.652 0.702 0.686 0.669 0.677 0.677 1.531 1.093 0.551 58.2 40.9 0.9 0.35 0.746 0.742 0.056 0.602 0.766 0.373 0.056 0.602 0.766
ACDCNN 342 342 684 239 1.5 0.9 102 240 -1.5 0.9 103 341 343 0.699 0.702 0.701 0.700 0.700 0.700 1.381 1.006 0.687 61.5 38.5 0.0 0.40 0.796 0.802 0.073 0.681 0.737 0.422 -0.110 0.751 0.670 S D T TP avg err FP TN avg err FN P N SEN SPE PPV NPV ACC accn RMSE MAE PCC Sc Ob1 Ob2 MCC AUC_R AUC_P THROC Sen Spe BMCC TH Sen Spe
KORPM 253 89 342 227 1.6 1.0 49 40 -0.7 0.5 26 276 66 0.897 0.449 0.822 0.606 0.781 0.673 1.382 0.983 0.488 64.0 35.7 0.3 0.39 0.797 0.917 0.400 0.719 0.708 0.413 0.795 0.502 0.955
KORPM* 253 89 342 228 1.6 1.0 50 39 -0.7 0.5 25 278 64 0.901 0.438 0.820 0.609 0.781 0.670 1.378 1.000 0.494 62.0 37.4 0.6 0.38 0.793 0.913 0.582 0.680 0.753 0.398 0.949 0.538 0.910
Cartddg 253 89 342 148 1.7 1.7 21 68 -0.7 2.6 105 169 173 0.585 0.764 0.876 0.393 0.632 0.675 3.552 2.604 0.448 46.8 41.8 11.4 0.31 0.740 0.890 -0.286 0.632 0.742 0.376 0.505 0.510 0.910
FoldX 253 89 342 124 1.8 0.9 16 73 -0.7 0.9 129 140 202 0.490 0.820 0.886 0.361 0.576 0.655 2.179 1.511 0.381 52.0 38.9 9.1 0.28 0.690 0.875 -0.231 0.577 0.742 0.323 0.178 0.455 0.899
Evo 253 89 342 154 1.7 1.0 39 50 -0.6 0.6 99 193 149 0.609 0.562 0.798 0.336 0.596 0.585 1.745 1.250 0.312 57.0 37.7 5.3 0.15 0.654 0.854 0.253 0.545 0.685 0.245 1.159 0.257 0.966
PopMs 253 89 342 174 1.7 1.2 30 59 -0.7 0.6 79 204 138 0.688 0.663 0.853 0.428 0.681 0.675 1.600 1.156 0.471 55.6 43.6 0.9 0.31 0.753 0.893 0.045 0.652 0.708 0.344 0.230 0.522 0.865
Dynamut2 253 89 342 44 1.9 1.6 22 67 -0.7 0.6 209 66 276 0.174 0.753 0.667 0.243 0.325 0.463 2.371 1.848 0.045 41.5 44.4 14.0 -0.08 0.439 0.720 -0.920 0.656 0.303 0.113 0.858 0.047 1.000
DDGun3D 253 89 342 187 1.6 1.0 42 47 -0.7 0.6 66 229 113 0.739 0.528 0.817 0.416 0.684 0.634 1.452 1.052 0.529 60.8 38.6 0.6 0.25 0.704 0.884 0.065 0.648 0.674 0.328 0.522 0.387 0.955
TherNet 253 89 342 170 1.8 1.2 32 57 -0.7 0.5 83 202 140 0.672 0.640 0.842 0.407 0.664 0.656 1.535 1.095 0.467 57.6 41.5 0.9 0.28 0.720 0.879 0.062 0.628 0.764 0.345 0.062 0.628 0.764
ACDCNN 253 89 342 200 1.6 1.0 50 39 -0.6 0.4 53 250 92 0.791 0.438 0.800 0.424 0.699 0.614 1.410 1.026 0.584 60.5 39.5 0.0 0.23 0.746 0.903 0.177 0.640 0.730 0.378 0.449 0.407 0.989 S D T TP avg err FP TN avg err FN P N SEN SPE PPV NPV ACC accn RMSE MAE PCC Sc Ob1 Ob2 MCC AUC_R AUC_P THROC Sen Spe BMCC TH Sen Spe
KORPM 89 253 342 37 0.6 0.4 23 230 -1.6 0.9 52 60 282 0.416 0.909 0.617 0.816 0.781 0.662 1.279 0.919 0.571 67.8 31.6 0.6 0.37 0.813 0.546 -0.437 0.742 0.767 0.473 -0.279 0.663 0.830
KORPM 89 253 342 36 0.6 0.4 21 232 -1.6 0.9 53 57 285 0.404 0.917 0.632 0.814 0.784 0.661 1.283 0.938 0.577 67.3 31.9 0.9 0.38 0.810 0.546 -0.630 0.787 0.723 0.481 -0.430 0.697 0.814
Cartddg 89 253 342 50 0.7 1.3 21 232 -1.7 3.0 39 71 271 0.562 0.917 0.704 0.856 0.825 0.739 3.321 2.661 0.675 57.9 40.4 1.8 0.52 0.843 0.643 -1.696 0.820 0.767 0.567 -0.715 0.719 0.866
FoldX 89 253 342 64 0.7 0.6 61 192 -1.9 1.1 25 125 217 0.719 0.759 0.512 0.885 0.749 0.739 1.479 1.060 0.647 68.1 30.1 1.8 0.44 0.804 0.588 0.130 0.708 0.802 0.476 0.130 0.708 0.802
Evo 89 253 342 55 0.6 0.5 63 190 -1.7 0.9 34 118 224 0.618 0.751 0.466 0.848 0.716 0.684 1.355 0.995 0.570 66.4 32.2 1.5 0.34 0.761 0.500 -0.119 0.674 0.731 0.368 0.226 0.517 0.846
PopMs 89 253 342 55 0.7 0.5 70 183 -1.7 1.2 34 125 217 0.618 0.723 0.440 0.843 0.696 0.671 1.561 1.138 0.479 57.6 41.2 1.2 0.31 0.739 0.438 -0.121 0.753 0.617 0.350 0.250 0.472 0.862
Dynamut2 89 253 342 28 0.9 0.6 18 235 -1.6 0.9 61 46 296 0.315 0.929 0.609 0.794 0.769 0.622 1.200 0.887 0.629 67.3 31.9 0.9 0.31 0.796 0.551 -0.470 0.764 0.715 0.432 -0.414 0.730 0.747
DDGun3D 89 253 342 46 0.7 0.5 63 190 -1.6 0.9 43 109 233 0.517 0.751 0.422 0.815 0.690 0.634 1.416 1.026 0.552 62.9 36.3 0.9 0.25 0.712 0.400 -0.094 0.685 0.640 0.318 -0.449 0.910 0.435
TherNet 89 253 342 53 0.7 0.5 70 183 -1.7 1.1 36 123 219 0.596 0.723 0.431 0.836 0.690 0.659 1.528 1.091 0.464 58.8 40.4 0.9 0.29 0.709 0.411 -0.010 0.618 0.708 0.320 -0.340 0.899 0.451
ACDCNN 89 253 342 39 0.7 0.4 52 201 -1.7 1.0 50 91 251 0.438 0.794 0.429 0.801 0.702 0.616 1.352 0.987 0.614 62.6 37.4 0.0 0.23 0.750 0.452 -0.175 0.730 0.636 0.376 -0.320 0.933 0.482
(```
KORPM results trained with balanced data [../Id25c03_1merNCLB_Ssym.txt](Id25c03_1merNCLB_Ssym.txt) set exluding all proteins with a sequence identity <0.25 with Ssym proteins
KORPM* results trained with balanced datased [../Id25c03_1merNCLB.txt](Id25c03_1merNCLB.txt) in where just the Ssym mutations where excluded (default korpm weights)
*NOTE the Ssym original dataset was updated according to the last Thermomutdb database version 3.
```sh
PDB MUT OLD New MEDLINE REFERENCE http://biosig.unimelb.edu.au/thermomutdb/
1BNI IA96V -3.100 -0.90 ref 2669964 reports -0.90 1569557 reports -0.95 9551101 -0.80
1BNI SA91A -2.400 -1.800 ref 14516751 reports -1.90 1569558 reports -1.94
1L63 SA44T 0.000 0.010 ref 8289284
1L63 SA38N 0.000 -0.010 ref 1911773
1L63 LA91A -3.900 -2.600 ref 10545167
1L63 AA130S 1.000 -1.0 ref 8218201
1LZ1 VA2G -1.300 -2.290 ref 11087397
1LZ1 VA2L 0.300 -0.050 ref 11087397
1LZ1 IA56T -4.300 -3.600 ref 9010773 ref 10556244
1LZ1 VA74I -1.900 0.450 ref 11087397
1LZ1 VA74L -0.400 0.190 ref 11087397
1LZ1 VA74M -0.400 0.650 ref 11927576 and 11087397
1LZ1 VA74F 0.000 -0.290 ref 11927576 and 11087397
1LZ1 VA110G -2.200 0.480 ref 11927576 and 11087397
1LZ1 VA110I -0.800 0.860 ref 11927576 and 11087397
1LZ1 VA110F -1.900 -0.050 ref 11927576 and 11087397
2LZM IA3C 0.000 1.200 ref 3405287 for -1.2 SH +1.2 S-S the mutat has S-S
2LZM RA119E 0.000 -0.040 ref 1942034 (trying to avoid 0 for the binary clasification)
4LYZ GA49A -0.700 -1.900 ref 11112507 and ref 8771183
4LYZ GA71A -2.100 -0.380 ref 11112507
4LYZ GA102A -1.200 0.020 ref 11112507
4LYZ GA117A -0.800 -1.460 ref 11112507
1RN1 QC25K 1.400 0.930 ref 2663837
2LZM RA96K 0.000 -0.001 avoiding zero for the binary clasification
1L63 SA44E 0.000 0.001 avoiding zero for the binary clasification
2LZM KA60P 0.000 -0.001 avoiding zero for the binary clasification