Table 3.
Metrics for models predicting Asn degradation in validation set. The letters A, B and C refer to the different sets of predictors. ‘A’ represents the SASA-group (including ASA and ASA(n + 1)), ‘B’ denotes the Static-group (including ASA, ASA(n + 1), Amide_pka, and Area_amide), and ‘C’ refers to the Dynamic-group (including ASA, SC_rmsd, Ca_rmsd, and Amide_pKa). The sequence-based approach classifies NG and NS as the only two motifs susceptible to degradation.10
| Homology Model |
Low MD 50 Confs. |
Low MD 400 Confs. |
ST pH6 |
ST pH8.5 |
MD Sim 200ns |
Seqence- based |
ST pH8.5 Thres 0.3 | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Predictor | A | B | A | B | C | A | B | C | C | C | C | NG, NS | C |
| TPR (Sensitivity, %) | 40.7 | 47.3 | 45.3 | 58.0 | 47.3 | 49.3 | 53.3 | 62.0 | 50.7 | 58.0 | 50.0 | 52.0 | 80.0 |
| TNR (Specificity, %) | 82.7 | 71.6 | 83.1 | 83.1 | 76.9 | 84.4 | 82.7 | 80.9 | 82.2 | 83.6 | 85.8 | 90.2 | 72.4 |
| Error (%) | 34.1 | 38.1 | 32.0 | 26.9 | 34.9 | 29.6 | 29.1 | 26.7 | 30.4 | 26.7 | 28.5 | 25.1 | 24.5 |
| Precision (%) | 64.3 | 52.6 | 64.2 | 69.6 | 57.7 | 71.6 | 67.2 | 68.4 | 65.5 | 70.2 | 70.1 | 78.0 | 66.3 |
| F1-score (%) | 48.8 | 49.8 | 53.1 | 63.3 | 52.0 | 56.5 | 59.5 | 65.0 | 57.1 | 63.5 | 58.4 | 62.4 | 72.1 |
| Balanced accuracy (%) | 61.7 | 59.4 | 64.2 | 70.6 | 62.1 | 66.8 | 68.0 | 71.4 | 66.4 | 70.8 | 67.9 | 71.1 | 76.2 |
| Total accuracy (%) | 65.9 | 61.9 | 68.0 | 73.1 | 65.1 | 70.4 | 70.9 | 73.3 | 69.6 | 73.3 | 71.5 | 74.9 | 75.5 |
| AUC in (0,1) | 0.72 | 0.63 | 0.74 | 0.75 | 0.70 | 0.74 | 0.77 | 0.80 | 0.75 | 0.84 | 0.77 | 0.71 | 0.84 |