Macromolecular docking is the computational modelling of the quaternary structure of complexes formed by two or more interacting biological macromolecules. AutoDock is a suite of automated docking tools designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.
In this tutorial, we will cover the following topics
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a brief introduction to protien-ligand docking
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preparing a protein and ligand for docking using AutoDock Tools
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running docking jobs on LONI and LSU HPC systems
Note: AutoDock and AutoDock Tools are free software that can be downloaded from http://autodock.scripps.edu. Users can run AutoDock on their desktop or laptop but this tutorial will only include examples for running autodock on LONI or LSU HPC systems. However if you have successfully configured autodock and autogrid programs (will not be covered here) on your laptop, you are welcome to use your laptop for running the examples in lieu of LONI or LSU HPC compute resources.
Prerequisites:
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LONI or LSU HPC accounts for running autodock.
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Laptop equipped with an SSH client such as putty.
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Users need to download and install AutoDock Tools (MGL Tools 1.5.4) on their Laptop from http://mgltools.scripps.edu/downloads. You do not need to download/install AutoDock for this training.
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Background in Computational Chemistry/Biology is preferred.
Registration: Please visit http://www.hpc.lsu.edu/training/tutorials/reservation-forms/spring2012-autodock.php