Table 1. Nine-State Results for Trialanine Using the Amber99SB Force Field and TIP3P Water with Both MD Prior and Random Coil Priora.
| α |
β |
PII |
|||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | |||
| Amber 99SB & TIP3P | A-α-II | A-α-I | A-α-III | A-β-II | A-β-I | A-β-III | A-PII-II | A-PII-I | A-PII-III | χ2 | |
| MD Prior | Winitial(σ) | 2.1(20) | 2.7(20) | 4.8(20) | 5.4(20) | 10.7(20) | 16(20) | 10.3(20) | 19.8(20) | 28.1(20) | 10.52 |
| Wbayesian(σ) | 3.6(3.1) | 2.4(2) | 4(3.3) | 1.5(1.4) | 1.2(1.1) | 1.8(1.7) | 12.3(6.5) | 4.3(3.2) | 69.0(6.7) | 3.17 | |
| RC Prior | Winitial(σ) | 11.1(20) | 11.1(20) | 11.1(20) | 11.1(20) | 11.1(20) | 11.1(20) | 11.1(20) | 11.1(20) | 11.1(20) | 14.63 |
| Wbayesian(σ) | 3.8(3.2) | 2.4(2.1) | 4.6(3.6) | 1.5(1.4) | 1.2(1.1) | 1.9(1.8) | 13.7(7.1) | 4.1(3.1) | 66.9(7.1) | 3.23 | |
a
Winitial refers to a priori knowledge about weights of n conformation substates of the peptide. Wbeysian refers to the current best estimate of substate weights and their confidence interval. χ2 = z–1∑j=1z(expDj – compDj)2/(σ2(expDj)) + σ2(compDj)).