Table 1.
Comparing AlGDock and YANK binding free energy estimates. The AlGDock free energies were calculated using different weighting schemes. RMSE is in units of kcal/mol.
| Full (24) | Active (11) | Inactive (13) | |||||
|---|---|---|---|---|---|---|---|
|
| |||||||
| Weighting Scheme | Linear Regression | RMSE | R | RMSE | R | RMSE | R |
|
| |||||||
| a | y=1.10x+0.77 | 1.48(0.23) | 0.91(0.02) | 1.13(0.20) | 0.79(0.04) | 1.72(0.33) | 0.93(0.03) |
| b | y=1.14x+0.62 | 1.57(0.27) | 0.91(0.02) | 1.23(0.18) | 0.75(0.05) | 1.81(0.45) | 0.93(0.04) |
| c | y=1.13x+0.56 | 1.59(0.23) | 0.90(0.02) | 0.77(0.08) | 0.90(0.03) | 2.04(0.36) | 0.91(0.03) |
| d | y=1.17x+0.38 | 1.76(0.27) | 0.90(0.02) | 0.98(0.16) | 0.87(0.04) | 2.22(0.44) | 0.91(0.03) |
| e | y=1.18x+0.82 | 1.53(0.24) | 0.92(0.02) | 0.93(0.31) | 0.90(0.02) | 1.90(0.29) | 0.92(0.03) |
| f | y=1.18x+0.66 | 1.49(0.21) | 0.92(0.02) | 0.94(0.36) | 0.93(0.01) | 1.83(0.27) | 0.92(0.03) |
| c1 | y=1.09x+0.52 | 1.75(0.26) | 0.87(0.02) | 0.89(0.10) | 0.87(0.03) | 2.23(0.39) | 0.87(0.03) |
1
Using only snapshots from YANK calculations with active ligands.