Table V.
Ab initio modeling results by QUARK and Rosetta.
| First (best in top 5) cluster center model | |||||||
|---|---|---|---|---|---|---|---|
| RMSD | TM-score | GDT-TS | MaxSub | HB-score | Time | ||
| 51 small proteins with [70–100) residues | Rosetta | 10.1Å(8.5Å) | 0.350(0.393) | 0.381(0.418) | 0.291(0.337) | 0.442(0.491) | 25.0hr |
| QUARK | 9.1Å(7.7Å) | 0.404(0.441) | 0.428(0.466) | 0.349(0.389) | 0.503(0.538) | 37.7hr | |
| QUARK-ha | 6.4Å(4.6Å) | 0.585(0.667) | 0.602(0.691) | 0.552(0.635) | 0.610(0.681) | 37.7hr | |
| 94 medium proteins with [100–150] residues | Rosetta | 13.0Å(11.5Å) | 0.317(0.346) | 0.293(0.318) | 0.224(0.247) | 0.410(0.453) | 63.3hr |
| QUARK | 12.5Å(10.7Å) | 0.334(0.374) | 0.310(0.342) | 0.237(0.268) | 0.471(0.504) | 79.5hr | |
| QUARK-ha | 8.6Å(6.6Å) | 0.491(0.541) | 0.439(0.483) | 0.362(0.410) | 0.449(0.503) | 79.5hr | |
a
QUARK simulation using fragments without removing homologous templates to the query sequence. However, the target proteins themselves, if existing in the library, were excluded.