Table 3 Comarison of MDPA predictions of human lysozyme (PDB code: 1LZS) undergoing different conformation changes by applying the lowest frequency normal mode motion with different amplitudes
From: A multilayer dynamic perturbation analysis method for predicting ligand–protein interactions
Amplitude | Entry | Ligand-binding Site Prediction | Ligand Overlap | ||
|---|---|---|---|---|---|
Precision | Recall | Precision | Recall | ||
100 | 00 | 0.29 | 1.00 | 0.83 | 1.00 |
01 | 0.27 | 1.00 | 0.75 | 1.00 | |
02 | 0.27 | 1.00 | 0.75 | 1.00 | |
03 | 0.29 | 1.00 | 0.80 | 1.00 | |
04 | 0.31 | 1.00 | 0.86 | 1.00 | |
05 | 0.31 | 1.00 | 0.77 | 1.00 | |
06 | 0.31 | 1.00 | 0.75 | 1.00 | |
07 | 0.31 | 1.00 | 0.75 | 1.00 | |
08 | 0.31 | 1.00 | 0.86 | 1.00 | |
09 | 0.29 | 1.00 | 0.86 | 1.00 | |
10 | 0.27 | 1.00 | 0.75 | 1.00 | |
11 | 0.27 | 1.00 | 0.75 | 1.00 | |
200 | 00 | 0.31 | 1.00 | 0.80 | 1.00 |
01 | 0.31 | 1.00 | 0.82 | 1.00 | |
02 | 0.29 | 1.00 | 0.83 | 1.00 | |
03 | 0.31 | 1.00 | 0.80 | 1.00 | |
04 | 0.33 | 1.00 | 0.75 | 1.00 | |
05 | 0.33 | 1.00 | 0.82 | 1.00 | |
06 | 0.33 | 1.00 | 0.80 | 1.00 | |
07 | 0.31 | 1.00 | 0.82 | 1.00 | |
08 | 0.31 | 1.00 | 0.75 | 1.00 | |
09 | 0.29 | 1.00 | 0.80 | 1.00 | |
10 | 0.29 | 1.00 | 0.83 | 1.00 | |
11 | 0.31 | 1.00 | 0.82 | 1.00 | |