Table 2.
Benchmark.
| Assembly | Component modeling | Coarse-grained sampling | Fine-grained sampling | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Assembly (name, PDB entry) | # component s | % Seq. Id. average rangea | Cα RMSD (Å) average rangeb | NO3.5 (%) average rangeb | Rankc | Optimization (assembly placement score) | Rankc | Optimization (assembly placement score) | |||
| Chaperonin GroEL, 1oel | 3 domains | 65 | 60–72 | 0.9 | 0.2–1.0 | 96 | 92–100 | 1 | (2.6, 13) | 1 | (2.6, 13) |
| SUMO-RanGAP1-Ubc9-Nup358/RanBP 2 complex, 1z5s | 4 proteins | 100 | 100– 100 | 0.0 | 0.0–0.0 | 10 0 |
100–100 | 1 | (5.9, 113) | 1 | (5.0, 67) |
| SUMO-RanGAP1-Ubc9-Nup358/ArnBP2 complex, 1z5s | 4 proteins | 37 | 18–56 | 7.9 | 1.2–15.0 | 52 | 13–98 | 3 | (7.7, 92) | 3 | (6.4, 62) |
| Dihydropyrimid ine Dehydrogenase, 1gte | 5 domains | 100 | 100– 100 | 0.0 | 0.0–0.0 | 10 0 |
100–100 | 1 | (2.6,4) | 1 | (2.6, 4) |
| Archaeon Methanopyrus kandleri,1e6v | 6 proteins | 61 | 57–68 | 0.0 | 0.0–0.0 | 10 0 |
100–100 | 1 | (2.5, 8) | 1 | (2.5, 8) |
| Arp2/3 complex, 1tyq | 7 proteins | 51 | 16–99 | 7.9 | 0.4–21.4 | 70 | 38–100 | 10 | (10.8, 136) | 4 | (7.1, 25) |
a
The average, minimum, and maximum percentage of sequence identity between the assembly components and their templates.
b
The average, minimum, and maximum Cα RMSD and native overlap NO3.5 between the modeled components superposed on their corresponding component in the native assembly.
c
The rank of a model with mapping score 0.