Extended Data Fig. 3: Docking and virtual screening metrics.
From: An open-source drug discovery platform enables ultra-large virtual screens
a, Scaling behaviour of VFVS using QuickVina 2 as the docking program. Tests with up to 30,000 cores on two local computer clusters (LC1 and LC2) and up to 160,000 CPUs on the GCP were carried out. The measured speedup is linear. DOVIS 2.0, an alternative software for virtual screenings on Linux computer clusters using AutoDock, was shown to exhibit near-linear scaling only up to 256 cores, as previously reported4. b, The computational time required (in days) for VFVS to complete virtual screens of different sizes, as a function of the number of CPUs being used in parallel. Each curve corresponds to a input ligand library with a different size, and the average computation time per ligand was assumed to be 5 s per ligand. c, Docking time of an average-sized ligand on a modern Intel CPU (using only a single core) as a function of the exhaustiveness parameter for different docking programs supported by VFVS. The bar plot in the inset shows the slope of the curves, which corresponds to the docking time per exhaustiveness unit. The test ligand that was used for this purpose is given by the SMILES code CN1CCN(S(=O)(=O)N2CCN(C(=O)CCCNC(=O)C3CC3)CC2)CC1. More detailed benchmarks can be found in publications related to these docking programs5,12,13,14,15,16,17.
