Table V.
RMSD of models selected by different scoring functions.a
| Models | RMSDinit | RMSDmin | RAPDF/HBb | ROSETTA_softb | ROSETTA_subb | RAPDF/HBEMc |
|---|---|---|---|---|---|---|
| a. Small, globular protein data set | ||||||
| 1cy5_1 | 2.77 | 1.77 | 2.34 (5) | 2.29 | 2.14 | 2.17 |
| 1cy5_2 | 1.90 | 1.31 | 1.51 (4) | 1.39 | 1.64 | 1.44 |
| 1fm0 | 2.23 | 1.12 | 1.33 (5) | 1.46 | 1.35 | 1.25 |
| 1gxu | 1.81 | 1.09 | 1.31 (2) | 1.59 | 1.45 | 1.29 |
| 1k5n | 2.05 | 1.69 | 2.00 (1) | 2.29 | 2.06 | 1.82 |
| 1mfg_1 | 2.41 | 2.19 | 2.90 (0) | 2.67 | 2.31 | 2.53 |
| 1mfg_2 | 1.73 | 1.16 | 1.21 (5) | 1.61 | 1.53 | 1.42 |
| 1opd | 3.22 | 2.32 | 2.61 (2) | 2.90 | 3.41 | 3.27 |
| 1r6j_1 | 2.15 | 1.07 | 1.83 (2) | 2.08 | 1.24 | 1.33 |
| 1r6j_2 | 1.77 | 1.32 | 2.13 (0) | 1.79 | 1.62 | 1.81 |
| 1urr | 2.01 | 0.96 | 1.59 (1) | 2.35 | 1.03 | 1.55 |
| 1wm3_1 | 2.38 | 1.85 | 2.20 (3) | 2.26 | 2.26 | 2.30 |
| 1wm3_2 | 1.63 | 1.05 | 1.35 (1) | 1.73 | 1.71 | 2.15 |
| 1xmt | 2.69 | 1.94 | 3.20 (0) | 3.18 | 2.52 | 2.91 |
| b. CASPR data set | ||||||
| 1xe1 | 1.26 | 0.94 | 1.05 (2) | 1.17 | 1.17 | 0.87 |
| 1vm0 | 3.00 | 2.50 | 2.98 (1) | 3.00 | 2.64 | 2.84 |
| 1vla | 2.26 | 2.20 | 2.26 (0) | 2.26 | 2.29 | 2.35 |
| 1whz | 1.69 | 0.75 | 0.91 (5) | 1.00 | 1.00 | 0.79 |
| 1tvg | 4.29 | 3.15 | 4.38 (0) | 3.48 | 4.21 | 4.09 |
| 1xg8 | 4.68 | 3.88 | 4.50 (2) | 5.36 | 5.36 | 4.97 |
| 1o13 | 1.90 | 1.51 | 1.78 (2) | 2.96 | 1.88 | 2.14 |
The items listed include the model name, initial RMSD in the REMD simulation, minimum RMSD can be found in the REMD simulation, RMSD of the best model ranked by RAPDF/HB score, two ROSETTA scores and RAPDF/HB score after energy minimization.
RMSD here denotes SSE-RMSD as in Table III. The RMSD values that are at least 0.2 Å lower than the initial values are in bold.
For these three scoring functions, the best model was selected using the following procedure. First, the best scoring model in each of the 5 REMD trajectories at the lowest temperatures was determined by a given scoring function. Then taking these five models the one with the lowest SSE-RMSD was selected as the best model. Note that for the RAPDF/HB scoring function the number of models with lower SSE-RMSD than the initial values is listed in parentheses.
In the RAPDF/HBEM scoring scheme, the 100 top-scoring structures ranked by the RAPDF/HB function in each of 5 replica simulations used (a total of 500 structures) were subjected to energy minimization. The RAPDF/HB scores were then calculated for the minimized structures. The SSE-RMSD of the best model selected by the same procedure as described above is listed in the last column.