title: 1001 Ways to run AutoDock Vina for virtual screening.
abstract: Large-scale computing technologies have enabled high-throughput virtual screening involving thousands to millions of drug candidates. It is not trivial, however, for biochemical scientists to evaluate the technical alternatives and their implications for running such large experiments. Besides experience with the molecular docking tool itself, the scientist needs to learn how to run it on high-performance computing (HPC) infrastructures, and understand the impact of the choices made. Here, we review such considerations for a specific tool, AutoDock Vina, and use experimental data to illustrate the following points: (1) an additional level of parallelization increases virtual screening throughput on a multi-core machine; (2) capturing of the random seed is not enough (though necessary) for reproducibility on heterogeneous distributed computing systems; (3) the overall time spent on the screening of a ligand library can be improved by analysis of factors affecting execution time per ligand, including number of active torsions, heavy atoms and exhaustiveness. We also illustrate differences among four common HPC infrastructures: grid, Hadoop, small cluster and multi-core (virtual machine on the cloud). Our analysis shows that these platforms are suitable for screening experiments of different sizes. These considerations can guide scientists when choosing the best computing platform and set-up for their future large virtual screening experiments.
authors.affiliation: Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands. mmajid@gmail.com.
authors.forename: Mohammad Mahdi
authors.initials: MM
authors.lastname: Jaghoori
authors.affiliation: Department of Medical Biochemistry, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands.
authors.forename: Boris
authors.initials: B
authors.lastname: Bleijlevens
authors.affiliation: Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands.
authors.forename: Silvia D
authors.initials: SD
authors.lastname: Olabarriaga
mesh_terms: D017076:Computer-Aided Design / Q000191:economics; D062313:Databases, Pharmaceutical; D055808:Drug Discovery / Q000191:economics / Q000379:methods; D006801:Humans; D008024:Ligands; D062105:Molecular Docking Simulation; D057105:Nuclear Receptor Subfamily 4, Group A, Member 1 / Q000378:metabolism; D011506:Proteins / Q000378:metabolism; D015203:Reproducibility of Results; D012984:Software / Q000191:economics; D014584:User-Computer Interface
chemical_list: D008024:Ligands; C539821:NR4A1 protein, human; D057105:Nuclear Receptor Subfamily 4, Group A, Member 1; D011506:Proteins
keywords: AutoDock Vina; Grid computing; Hadoop; High-performance computing; Multi-core; Reproducibility; Virtual screening