Table 5 Docking calculation times and acceleration rates for three proteins of different sizes.
From: Protein-protein docking on hardware accelerators: comparison of GPU and MIC architectures
| Â | Â | Small | Medium | Large | |||
|---|---|---|---|---|---|---|---|
Receptor (#residues) | GRB2 C-ter SH3 domain (61) | CCS metallochaperone (249) | Nitrogenase Mo-Fe protein (2026) | ||||
Ligand (#residues) | Vav N-ter SH3 domain (70) | SOD1 superoxide dismutase (153) | Nitrogenase Fe protein (578) | ||||
PDB ID | [PDB:1GCQ] | [PDB:1JK9] | [PDB:1N2C] | ||||
FFT size | 80 × 80 × 80 | 128 × 128 × 128 | 216 × 216 × 216 | ||||
Docking time [second] (vs. 1CPU) | 1CPU | 38.3 | (1.0×) | 186.4 | (1.0×) | 1105.6 | (1.0×) |
|  | 8CPUs | 8.4 | (4.6×) | 38.5 | (4.8×) | 177.5 | (6.2×) |
|  | GPU | 5.8 | (6.6×) | 10.8 | (17.3×) | 62.2 | (17.8×) |
|  | MICoffload | 58.7 | (0.7×) | 77.0 | (2.4×) | 180.6 | (6.1×) |
|  | MICnative | 7.6 | (5.0×) | 26.8 | (7.0×) | 310.5 | (3.6×) |