TABLE 6.
Comparision of All-Atom Average RMSDs from the Native Crystal Structures for Both the CG Model and the Full-Atom Models. All RMSDs Were Obtained from All CG Atoms (Full-Atom Calculation Using the Same Atom Set as CG Model)
| RMSD (Å) | |||
|---|---|---|---|
| PDB ID | CG model | full-atom implicit water model (amber99sb ff) | full-atom explicit water model (amber99sb ff) |
| 157D | 3.644 | 5.609 | 2.260 |
| 1DQF | 2.478 | 3.274 | 1.935 |
| 1I9X | 3.236 | 3.956 | 1.780 |
| 2JXQ | 2.536 | 2.940 | 1.800 |
| 2K7E | 3.675 | 4.560 | 3.560 |
| 353D | 3.483 | 2.802 | 3.583 |
| 472D | 3.137 | 2.467 | 1.500 |
| 1F5G | 4.425 | 2.950 | 1.800 |
| 1KD3 | 4.570 | 3.740 | 2.560 |
| 1L2X | 2.840 | 2.890 | 2.730 |
| 1LNT | 4.751 | 2.610 | 1.880 |
| 1QCU | 1.669 | 2.560 | 2.210 |
| 1ZIH | 3.532 | 3.180 | 2.010 |
| 2AO5 | 3.326 | 2.090 | 1.350 |
| 1AL5 | 3.080 | 3.770 | 2.210 |
| Average | 3.359 | 3.293 | 2.211 |
a
All rmsd’s were obtained from all CG atoms (full-atom calculation using the same atom set as the CG model).