Table 2.
Machine learning-based affinity rankings for the LysM2 domain of select Populus LysM-RLKs bound to CO. “Unscaled” indicates a model trained on raw, unnormalized features. “Reduced” indicates a model trained on a subset of features that had the highest Spearman correlation with the training data (experimental binding affinities of the PDBBind database). For each column, the proteins are listed, from top to bottom, in order of increasing binding affinity. (Abbrev.: BT=boosted trees; RF=random forest; SVM=support-vector machine; PtLYK1-L1 =PtLYK1-like1; PtLYK1-L2 =PtLYK1-like2; PtLYK1-L3 =PtLYK1-like3; PtLYK4-L1 =PtLYK4-like1; PtLYK4-L2 =PtLYK4-like2; PtLYK5-L1 =PtLYK5-like1; PtLYK5-L2 =PtLYK5-like2).
| Machine learning-based affinity rankings | |||||
|---|---|---|---|---|---|
| Reduced | |||||
| Ranking | BT | RF | SVM | BT | RF |
| 1° | PtLYK1-L2 (8.8) | PtLYK5-L1 (9.2) | PtLYK1-L2 (9.0) | PtLYK1-L2 (8.7) | PtLYK5-L1 (9.5) |
| 2° | PtLYK5-L1 (8.2) | PtLYK1-L2 (9.0) | PtLYK5-L1 (8.3) | PtLYK5-L1 (8.2) | PtLYK1-L2 (9.0) |
| 3° | PtLYK1-L3 (7.5) | PtLYK1-L3 (7.8) | PtLYK5-L2 (7.8) | PtLYK1-L3 (7.5) | PtLYK1-L3 (8.4) |
| 4° | PtLYK1-L1 (7.2) | PtLYK1-L1 (7.2) | PtLYK1-L3 (7.5) | PtLYK1-L1 (7.1) | PtLYK1-L1 (7.5) |
| 5° | PtLYK5-L2 (6.6) | PtLYK5-L2 (6.5) | PtLYK1-L1 (7.0) | PtLYK5-L2 (6.6) | PtLYK5-L2 (6.6) |
| 6° | PtLYK4-L2 (4.4) | PtLYK4-L2 (4.7) | PtLYK4-L2 (4.8) | PtLYK4-L2 (4.3) | PtLYK4-L2 (4.6) |
| 7° | PtLYK4-L1 (3.7) | PtLYK4-L1 (3.6) | PtLYK4-L1 (4.2) | PtLYK4-L1 (3.9)) | PtLYK4-L1 (3.8) |
| Unscaled | |||||
| Reduced | |||||
| Ranking | SVM | BT | RF | BT | RF |
| 1° | PtLYK1-L2 (8.5) | PtLYK1-L2 (6.1) | PtLYK1-L2 (6.2) | PtLYK1-L2 (6.0) | PtLYK1-L2 (6.4) |
| 2° | PtLYK5-L1 (7.4) | PtLYK5-L1 (5.8) | PtLYK5-L1 (5.8) | PtLYK5-L1 (5.8) | PtLYK4-L2 (5.9) |
| 3° | PtLYK1-L3 (7.1) | PtLYK1-L3 (5.6) | PtLYK1-L1 (5.6) | PtLYK1-L3 (5.6) | PtLYK5-L1 (5.8) |
| 4° | PtLYK1-L1 (6.9) | PtLYK4-L2 (5.3) | PtLYK4-L2 (5.5) | PtLYK1-L1 (5.4) | PtLYK1-L1 (5.5) |
| 5° | PtLYK5-L2 (6.8) | PtLYK5-L2 (5.2) | PtLYK1-L3 (5.4) | PtLYK5-L2 (5.4) | PtLYK1-L3 (5.4) |
| 6° | PtLYK4-L2 (4.7) | PtLYK1-L1 (5.2) | PtLYK5-L2 (5.1) | PtLYK4-L2 (5.2) | PtLYK5-L2 (5.1) |
| 7° | PtLYK4-L1 (4.0) | PtLYK4-L1 (4.7) | PtLYK4-L1 (4.8) | PtLYK4-L1 (4.3) | PtLYK4-L1 (5.1) |