Software AutoDock Gateway | EGI Applications Database

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Applications Database
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Applications Database
Supporting
Applications Database
Supporting

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Name:AutoDock Gateway

Description:Science Gateway for molecular docking simulations using AutoDock

Abstract: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. 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.