Table IV.
Comparison of Flexible Docking for Ensembles Generated with BP-Dock vs Backrub
| RosettaLigand score (kcal/mol) |
X-Score (kcal/mol) |
||||||||
|---|---|---|---|---|---|---|---|---|---|
| protein | peptide | peptide classification |
peptide binding specificity |
rigid bound |
BP-Dock unbound |
Backrub unbound |
rigid bound |
BP-Dock unbound |
Backrub unbound |
| PSD-95 | KQTSV | I | I | –230.78 | –273.03 | –221.83 | –7.27 | –7.32 | –6.66 |
| PSD-95 | ATVRTYSC | II | I | NA | –271 | –223.04 | NA | –7.1 | –7.31 |
| GRIP | ATVRTYSC | II | II | –241.76 | –229.36 | –218.37 | –8.14 | –7.82 | –7.74 |
| GRIP | KQTSV | I | II | NA | –223.97 | –215.32 | NA | –7.1 | –7.15 |
| syntenin | DSVF | I | I and II both | –208.24 | –205.67 | –219.09 | –7.29 | –7.16 | –7.18 |
| syntenin | NEFYA | II | 1 and II both | –225.2 | –211.88 | –219.57 | –7.99 | –7.85 | –6.99 |
| CIPP | KQTSV | I | II | NA | –150.73 | –149.6 | NA | –7.08 | –7.23 |
| CIPP | EYLGLDVPV | II | II | NA | –151.87 | –154.6 | NA | –7.49 | –7.29 |