Table 2. Comparison between Random Coil (RC), Predicted Secondary Structure (Pred-SS), de novo MD (MD), and ENSEMBLE Optimized Pred-SS-ENS, and MD-ENS Ensemblesa.
| Aβ40 peptide | average
property |
|||
|---|---|---|---|---|
| ensemble type | RDC-PALES (Hz) | RDC-Local (Hz) | H2O NOEs | D2O NOEs |
| RC | 1.49 | 1.56 | 11.75 (0.47) | 4.61 (0.54) |
| Pred-SS | 1.54 | 1.36 | 4.68 (0.50) | 3.75 (0.54) |
| Pres-SS-ENS | 1.85 | 0.48 | 1.85 (0.68) | 3.54 (0.52) |
| MD | 2.22 | 1.88 | 1.15 (0.74) | 3.22 (0.55) |
| MD-ENS | 1.69 | 0.18 | 1.22 (0.70) | 3.66 (0.51) |
| Aβ42 peptide | average
property |
|||
|---|---|---|---|---|
| ensemble type | RDC-PALES (Hz) | RDC-Local (Hz) | H2O NOEs | D2O NOEs |
| RC | 1.35 | 1.42 | 7.25 (0.38) | 3.77 (0.44) |
| Pred-SS | 1.37 | 1.27 | 3.28 (0.52) | 1.26 (0.67) |
| Pres-SS-ENS | 1.17 | 0.42 | 1.81 (0.59) | 0.75 (0.76) |
| MD | 2.25 | 2.14 | 1.25 (0.67) | 0.58 (0.80) |
| MD-ENS | 2.13 | 0.33 | 1.51 (0.62) | 0.73 (0.76) |
a
We report RMSDs for the RDC calculator PALES and L-RDCs evaluated with ENSEMBLE using local alignments. The NOEs are back-calculated from the structural ensembles as described in Section 4. We evaluate the RMSD normalized by the largest NOE intensity, RMSDN and (correlation coefficient, r) with the H2O and D2O experiments. Some data reproduced from ref (14).