Table 4.
Evaluation of free energy estimators (native trajectory not included). Performance of SEEFs and PEEFs on the set not including native simulation. Performance is evaluated according to different methods (see Methods section). The lower part of the table refers to scores averaged over a moving window of 50 molecular dynamics snapshots.
| F1+F3+F4+F7 – no average | |||||
| Score funct. | logP(B1) | logP(B10) | F.E. | corr. coeff. | RMSD (Å) best score |
| contact + pc | -2.55 | -2.55 | 29.8 | 0.40 | 4.03 |
| FRST | -0.70 | -1.44 | 11.9 | 0.17 | 5.31 |
| MM | -0.34 | -0.64 | 2.3 | -0.07 | 7.45 |
| MM/GBSA | -1.20 | -1.70 | 23.2 | 0.38 | 4.37 |
| MM/PBSA | -0.04 | -1.02 | 15.1 | 0.32 | 8.90 |
| F1+F3+F4+F7 – with average | |||||
| Score funct. | logP(B1) | logP(B10) | F.E. | corr. coeff. | RMSD (Å) best score |
| contact + pc | -1.11 | -1.61 | 39.2 | 0.43 | 4.43 |
| FRST | -0.15 | -0.31 | 10.7 | 0.21 | 7.91 |
| MM | -0.07 | -0.08 | 0.0 | -0.14 | 8.59 |
| MM/GBSA | -1.20 | -1.83 | 34.5 | 0.44 | 4.37 |
| MM/PBSA | -0.85 | -1.23 | 24.6 | 0.38 | 4.80 |