AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. One AutoDock run can take significant computation time from minutes to several hours, depending on the complexity of the molecules. However, scientists typically have to run hundreds or thousands of experiments on the same molecules to get more accurate and reliable results. (As a consequence the same input is sent out a huge number of times but they all generate different outputs.) Deploying these applications on a desktop grid infrastructure, such asEDGeS@home, utilizing thousands of machines at the same time, allows harnessing sufficient computational power to undertake the simulations on a larger scale and in a much shorter timeframe. Once the docking simulations have finished, bio-scientist analyse and select the best (lowest energy) results, and visualise them using a variety of tools. An example for visualising the interaction of molecules is presented below (H5N1 (viral) and the Trichomonas vaginalis neuraminidase with the arginine triad).
Docking simulation programs have significant potential to contribute to a wide area of molecular and biomedical research including but not restricted to the study of molecular interactions in cancer, designing drug inhibitors for HIV, or assessing the environmental risks of veterinary medicines. In biological research, "wet laboratory" or in vitro methodologies require access to sophisticated and expensive equipment and considerable experimental time. Introduction and validation of computer based or in silico tools allow researchers to focus their resources and better plan experiments by allowing them to visualise large numbers of potential interactions and determine the best molecules to investigate in the laboratory. In silico experiments on the other hand, can be time consuming if run on conventional computers, taking weeks or even months to complete.
The AutoDock portal hosts the following workflows:
- AutoDock4 - Random blind docking requiring pdb input files
- AutoDock4 without AutoGrid - Random blind docking requiring pdbqt input files
- AutoDock Vina - Virtual screening of a library of ligands
The portal can be accessed at https://autodock-portal.sztaki.hu/