Table 5.
Root mean square deviations from experimental structures in PRIMO-MD simulations compared with all-atom simulations. Standard deviations are provided in parentheses.
| PDB | Res | avg. Cα RMSD (PRIMO) (Å) | Cα RMSD of avg. structure (PRIMO) (Å) | avg. Cα RMSD (CHARMM) (Å) | Cα RMSD of avg. structure (CHARMM) (Å) | RgPRIMO (Å) | RgCHARMM | Rgexp (Å) |
|---|---|---|---|---|---|---|---|---|
| 1VII | 36 | 3.3 (0.6) | 2.9 | 2.4 (0.4) | 2.3 | 9.4 (0.2) | 9.4 (0.2) | 9.4 |
| 3GB1 | 56 | 2.6 (0.5) | 2.3 | 1.1 (0.2) | 0.8 | 10.9 (0.1) | 10.4 (0.1) | 10.9 |
| 1BDD | 60 | 2.2 (0.3) | 1.8 | 2.0 (0.2) | 1.6 | 9.9 (0.1) | 9.4 (0.1) | 9.7 |
| 1D3Z | 76 | 3.3 (0.5) | 3.1 | 1.4 (0.2) | 1.3 | 11.9 (0.2) | 11.5 (0.1) | 12.0 |
| 2PTL | 78 | 2.5 (0.5) | 1.9 | 1.6 (0.3) | 1.3 | 11.6 (0.1) | 11.3 (0.1) | 11.5 |
| 1BTA | 89 | 2.6 (0.3) | 2.2 | 1.3 (0.2) | 1.2 | 12.1 (0.1) | 12.0 (0.1) | 11.8 |
| 1FKS | 107 | 3.5 (0.6) | 3.0 | 3.6 (0.7) | 2.7 | 13.1 (0.4) | 13.3 (0.2) | 13.7 |
| 1A2P | 110 | 3.9 (0.3) | 3.8 | 1.5 (0.3) | 1.2 | 14.0 (0.2) | 13.6 (0.1) | 13.6 |
| 2AAS | 124 | 4.4 (0.6) | 4.0 | 2.5 (0.4) | 2.0 | 14.9 (0.2) | 14.5 (0.2) | 14.2 |
| 1CYE | 129 | 2.6 (0.3) | 2.4 | 1.4 (0.2) | 1.2 | 13.4 (0.1) | 13.4 (0.1) | 13.3 |
| 2RN2 | 155 | 4.4 (0.6) | 3.8 | 2.0 (0.2) | 1.6 | 15.9 (0.2) | 15.3 (0.1) | 15.6 |