Skip to main content

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

   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×)
  1. The MIC native mode (MICnative) used an optimized numbers of threads, which were the largest numbers available for each protein size (small = 240 threads, medium = 171 threads, and large = 38 threads).