The AutoDock portal (based on WS-PGRADE) enables bio-scientists to run molecular docking simulations. The computation is powered by the EDGeS@home volunteer desktop grid.

The AutoDock portal can be accessed at https://autodock-portal.sztaki.hu/

Applications of the AutoDock Portal

The AutoDock portal hosts the following workflows:

AutoDock 4, AutoDock 4 without AutoGrid and AutoDock Vina. AutoDock4 - Random blind docking requiring pdb input files

This workflow requires pdb input files and docks a small ligand molecule on a larger receptor molecule structure in a Monte-Carlo simulation. The workflow uses version 4.2.3 of the AutoDock docking simulation package.

Users are expected to provide:

  • input files for AutoGrid (molecules in pdb format),
  • grid parameter (gpf) file,
  • docking parameter (dpf) file,
  • the number of simulations to be carried out,
  • the number of required results.

AutoDock4 without AutoGrid - Random blind docking requiring pdbqt input files

This workflow requires pdbqt input files and docks a small ligand molecule on a larger receptor molecule structure in a Monte-Carlo simulation. The workflow uses version 4.2.3 of the AutoDock docking simulation package.

Users are expected to provide:

  • a docking parameter file,
  • a zip file containing input files for AutoDock that were generated using version 4.2.3 of AutoGrid and the former docking parameter file,
  • the number of simulations to be carried out,
  • the number of required results.

AutoDock Vina - Virtual screening of a library of ligands

This workflow performs virtual screening of molecules using version 1.1.2 of AutoDock Vina. It docks a library of small ligands on a selected receptor molecule.

Users are expected to provide:

  • a config file for AutoDock Vina,
  • an input receptor molecule in PDBQT file format,
  • a zip file containing a number of ligands in PDBQT file format,
  • the number of parallel work units,
  • the number of required results.

 



       This project has received funding from the European Union's Seventh Framework Programme for research, technological development and demonstration under grant agreement no 283481.

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