Skip to main content

Table 3 Parallel and Serial Docking of 76 Receptor-Ligand complexes

From: Multilevel Parallelization of AutoDock 4.2

RMSD Comparisons
  s vs 1 s vs 4 1 vs 4
ave 0.414 0.439 0.366
rms 0.525 0.667 0.510
med 0.168 0.170 0.139
min 0.005 0.008 0.003
max 2.526 4.332 3.255
  1. 76 Receptor-Ligand complexes were docked using a 128 node (512 core) BG/P system using the benchmark parameters with modifications: ga_runs = 70, ga_num_evals = 5,000,000. Pairwise RMSD values between VN (serial) and VN (OMP = 1), VN (serial) and SMP (OMP = 4), and VN (OMP = 1) and SMP (OMP = 4) for both the lowest energy docked ligands and the lowest energy member of the largest ligand cluster were calculated. When the pairwise RMSD between lowest energy-lowest energy and largest cluster-largest cluster were not equal, the lesser RMSD value was used (approximately 20% of comparisons). Statistics for the three comparisons were calculated.