TABLE 1.
Energetic and stereochemical validation of missing fragments of PS1 protein.
| Missing region PS1 | Model | Software | QMEAN6 | Zscore | Ramachandran plot | |||
|---|---|---|---|---|---|---|---|---|
| Favorable region | Allowed region | Generously allowed region | Forbidden region | |||||
| Met1-Glu72 (M1-E72) | Unrefined | I-TASSER | 0.263 | −3.379 | 59.70% | 28.40% | 4.50% | 7.50% |
| Refined | FG-MD | 0.291 | −3.176 | 62.70% | 26.90% | 4.50% | 6.00% | |
| ModRefiner | 0.235 | −3.575 | 73.10% | 22.40% | 1.50% | 3.00% | ||
| Met1-Glu72 (M1-E72) | Unrefined | Phyre2 | 0.472 | −1.867 | 71.60% | 20.90% | 4.50% | 3.00% |
| Refined | FG-MD | 0.393 | −2.438 | 58.20% | 35.80% | 6.00% | 0.00% | |
| ModRefiner | 0.232 | −3.602 | 88.10% | 7.50% | 3.00% | 1.50% | ||
| Met1-Glu72 (M1-E72) | Unrefined | Quark ab initio | 0.368 | −2.62 | 84.00% | 10.70% | 5.30% | 0.00% |
| Refined | FG-MD | 0.286 | −3.209 | 65.70% | 20.90% | 7.50% | 6.00% | |
| ModRefiner | 0.309 | −3.041 | 86.60% | 10.40% | 1.50% | 1.50% | ||
| Ser290-Glu375 (S290-E375) | Unrefined | I-TASSER | 0.421 | −2.606 | 64.10% | 34.60% | 1.30% | 0.00% |
| Refined | FG-MD | 0.430 | −2.529 | 65.40% | 33.30% | 1.30% | 0.00% | |
| ModRefiner | 0.445 | −2.428 | 82.30% | 17.70% | 0.00% | 0.00% | ||
| Ser290-Glu375 (S290-E375) | Unrefined | Phyre2 | 0.450 | −2.374 | 60.30% | 23.10% | 11.50% | 5.10% |
| Refined | FG-MD | 0.449 | −2.377 | 56.40% | 32.10% | 11.50% | 0.00% | |
| ModRefiner | 0.455 | −2.374 | 83.30% | 12.80% | 1.30% | 2.60% | ||
| Ser290-Glu375 (S290-E375) | Unrefined | Quark ab initio | 0.404 | −2.74 | 79.10% | 13.90% | 7.00% | 0.00% |
| Refined | FG-MD | 0.353 | −3.151 | 53.80% | 41.00% | 2.60% | 2.60% | |
| ModRefiner | 0.376 | −2.969 | 76.90% | 17.90% | 3.80% | 1.30% | ||