Table S5.
Restrained docking results for E2A-HPr complex
| Restraints | Cluster rank | Cluster IRMSD | Cluster population | No. correlations | Execution time, min | |
| FMFT | PIPER | |||||
| No restraints | 2 | 5.25 | 201 | 8 | 12.32 | 96.15 |
| With restraints | 1 | 5.15 | 410 | 28 | 15.30 | 373.80 |
Results for docking HPr to the E2A protein using the FMFT algorithm with and without AIRs (Application 3). Use of experimental restraints significantly increased the population of the native cluster, bringing it to the top rank. Although accounting for the restraints increased the number of correlation terms from 8 to 28 in the scoring function, the execution time remained almost unchanged when using the FMFT algorithm, whereas it increased almost proportionally with the number of correlation function terms when using the Cartesian FFT method PIPER. In the table, Cluster rank shows the rank of the near-native model, assigned according to cluster population. Cluster IRMSD is the interface Cα RMSD of this near-native model. Cluster population is the number of poses in the cluster. No. correlations is the number of components in the correlation-based energy function.