Table II.
RMSDs of the CDR-H3 models versus the X-ray crystal structure
| Models | PMFa (kcal/mol) | Backbone RMSDb (Å) | All atoms RMSDc (Å) |
|---|---|---|---|
| Model a | 0.00 | 3.89 | 5.02 |
| Model b | 1.13 | 3.24 | 4.27 |
| Model c | 1.46 | 1.65 | 2.75 |
| Model d | 0.43 | 1.59 | 2.68 |
| Model e | 0.92 | 2.24 | 3.13 |
| Initiald | –e | 3.90 | 4.87 |
| AMA-II model1f | 1.59 | 3.69 | 5.16 |
| AMA-II model2f | 1.39 | 3.34 | 4.62 |
| AMA-II model3f | 2.69 | 3.74 | 4.78 |
| AMA-II model4f | 2.98 | 3.69 | 5.07 |
| AMA-II model5f | 1.54 | 3.42 | 5.03 |
| X-ray structure in chain B | 2.22 | 0.00 | 0.00 |
| X-ray structure in chain D | 3.28 | 0.35 | 1.78 |
aPMF values of the models and X-ray structure on the free energy landscape in Fig. 1. The reference is the PMF of model a.
bThe RMSD values of the backbone heavy atoms of the CDR-H3 loop in each model with reference to the X-ray crystal structure (chain B), where the Cα atoms in the residues other than the CDR-H3 loop from ArgH93 to TyrH102 were superimposed to the crystal structure (chain B).
cThe RMSD values of the all heavy atoms of the CDR-H3 loop in each model with reference to the X-ray crystal structure (chain B), where the Cα atoms in the residues other than the CDR-H3 loop from ArgH93 to TyrH102 were superimposed to the crystal structure (chain B).
dThe initial model as the Stage 1 result of AMA-II for the current McMD simulations.
eThe initial structure was not sampled by the current simulation, and it is out of the free energy landscape.
fThe Stage 2 models of AMA-II by the McMD computations.