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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.