AutoDock Gateway for Molecular Docking Simulations in Cloud Systems - Cloud Computing with e-Science Applications - page 222

single receptor. In this instance, parallelism is achieved by first breaking the
set of all ligands into equal-size disjoint subsets. Each compute job then uses a
different subset as an input. The ligands in each subset are simulated/docked
sequentially on the compute node using the single receptor; a postprocessing
stage can be used to compare the results from all compute jobs.
Researchers from the School of Life Sciences at the University of West-
minster in London have set up a novel screening system [ 7 ] to analyze
well-characterized protein-ligand interactions, for example, studying the
interrogation of enzymes and receptors of the protozoan Trichomonas vaginalis
(TV). TV is an important organism, with 180,000 million women affected
worldwide. It is also a proven cofactor for the acquisition of human immuno-
deficiency virus (HIV). Currently, only one drug is available, metronidazole,
and resistance has been reported. The cloning and publication of the TV
genome offers new options for drug/inhibitor detection utilizing bioinfor-
matics and molecular modeling tools.
Westminster researchers constructed an in silico small molecule library of
about 300,000 structures. Given a receptor file and the approximated position
and size for the active site, the whole library was planned to be screened against
the chosen receptor using the AutoDock Vina (http://vina.scripps.edu/)
molecular docking tool. Once operational, the system could easily be utilized
for other similar virtual screening experiments.
10.3.2 AutoDock Workflows
Three different parameter sweep workflows were developed (in the frame-
work of the EU FP7 ER-Flow project [ 8 ]) based on the AutoDock4 and
AutoDock Vina applications and the previously described scenarios: the
AutoDock workflow, the AutoDock without AutoGrid workflow, and the
AutoDock Vina workflow.
The AutoDock workflow requires PDB (Program Database) input files
(these are widely available in public databases), automatically converts these
files into PDBQT format (which is required by the AutoDock application),
calculates the docking space running the AutoGrid application, and docks
a small ligand molecule on a larger receptor molecule structure in a Monte
Carlo simulation. Finally, it returns the required number of lowest-energy-
level solutions. The workflow uses version 4.2.3 of the AutoDock docking
simulation package. Users of this workflow are expected to provide input
files for AutoGrid (molecules in PDB format), grid parameter file (GPF), dock-
ing parameter file (DPF), the number of simulations to be carried out, and
the number of required results. The workflow is shown in Figure 10.4. This
workflow is ideal for researchers who are less familiar with the AutoDock
suite and command line tools and require a high level of automation when
executing their experiments.
On the other hand, the AutoDock without AutoGrid workflow requires
the scientist to run scripts from the AutoGrid application on his or her own