Table 3 Predictive power of the differences between wild type and variant proteins for different structural properties.
Property | FPR | TPR | Best MCC | Threshold | MCC90 |
|---|---|---|---|---|---|
FoldX energy evaluation | |||||
Overall stability difference | 73 | 85 | 0.15 | -0.45 | 0.14 |
Overall stability diff. (surface) | 0 | 8 | 0.2 | 3.1 | 0.13 |
Overall stability diff. (buried) | 21 | 44 | 0.25 | 2.64 | 0.12 |
Backbone clash | 91 | 99 | 0.18 | -1.00 | -0.02 |
Backbone H bond | 59 | 83 | 0.26 | -0.025 | 0.06 |
Sidechain H bond | 79 | 92 | 0.18 | -0.13 | -0.14 |
Electrostatics | 6 | 18 | 0.18 | 0.15 | 0.16 |
Entropy main chain | 6 | 18 | 0.18 | 0.15 | 0.04 |
Entropy side chain | 64 | 74 | 0.11 | -0.125 | -0.05 |
Solvation hydrophobic | 57 | 75 | 0.19 | -0.15 | -0.03 |
Solvation polar | 22 | 36 | 0.15 | 0.20 | -0.05 |
Torsion clash | 1 | 3 | 0.07 | 1.00 | -0.05 |
Van der Waals contribution | 7 | 14 | 0.11 | 0.89 | 0.10 |
Van der Waals clash | 98 | 100 | 0.10 | -1.60 | 0.02 |
Entropy difference by sampling of possible side chain conformations | |||||
FoldX entropy difference | 85 | 92 | 0.11 | -1.85 | -0.02 |
FoldX entropy diff. (buried) | 96 | 100 | 0.14 | -2.70 | -0.05 |
FoldX entropy diff. (surface) | 37 | 57 | 0.20 | -0.10 | 0.02 |
Aggregation properties | |||||
Tango | 1 | 3 | 0.07 | 39.9 | 0 |
Tango (positive, more aggr.) | 14 | 22 | 0.10 | 16.37 | 0 |
Tango (negative, less aggr.) | 69 | 78 | 0.10 | -8.00 | 0 |
Waltz | 0 | 1 | 0.07 | 748.97 | 0 |
Waltz (positive, more aggr.) | 16 | 21 | 0.06 | 677.15 | 0 |
Waltz (negative, less aggr.) | 99 | 100 | 0.07 | -2412.78 | 0 |
Limbo | 17 | 33 | 0.18 | 5.45 | 0 |