TABLE 5.
Comparison of the programs colores and gmfit in terms of computation time and RMSD (Å)
|
colores
|
gmfit*
|
gmfit†
|
||||||
|---|---|---|---|---|---|---|---|---|
| PDB code | Time (s)‡ | RMSD (Å) | Times for each step (s)§ | Time (s)‡ | RMSD (Å) | Times for each step (s)§ | Time (s)‡ | RMSD (Å) |
| 1afw | 107.8 | 0.65 | 1.0, 2.7, 1.4 | 5.1 | 1.16 | 5.4, 2.7, 7.1 | 15.2 | 1.03 |
| 1nic | 94.6 | 1.85 | 1.2, 5.9, 4.9 | 12.0 | 1.89 | 5.6, 5.9, 16.0 | 27.5 | 1.77 |
| 7cat | 77.0 | 0.61 | 4.6, 12.9, 10.6 | 28.0 | 41.83 | 6.0, 12.9, 46.0 | 64.9 | 2.27 |
| 2rec | 142.8 | 0.33 | 0.1, 3.8, 37.7 | 41.6 | 2.91 | 0.1, 3.8, 110.9 | 114.8 | 2.29 |
*
Performance of the gmfit program using 8 GDFs for each subunit and 12 GDFs for a density map.
†
Performance of the gmfit program using 16 GDFs for each subunit and 12 GDFs for a density map.
‡
Total computation time.
§
Computation times for the three steps of gmfit: estimating the GMM from a subunit atomic model; estimating the GMM from a density map of the complex; and searching for the optimal configuration.