SI2011 Virtual Screening Using AutoDock Suite of Tools

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General Information

The track is geared towards both beginning and intermediate level users of AutoDock for the development of inhibitors to proteins and other validated pharmaceutical targets. Those interested in cheminformatics approaches in the post-processing of virtual screening results would also benefit. Those interested in the use of more advanced techniques in the evaluation of binding rate constant should consider Track 2. Users wishing to focus on customization of a graphical user interface should also consider Track 6, where customizable workflow tools for virtual screening will be introduced.

Participants will learn (1) how to set up AutoDock 4.2 and AutoDock Vina based dockings using AutoDockTools, (2) how to setup virtual screening experiments using a new tool Raccoon and how to analyze the results using another new tool Fox, (3) how to find potential binding sites with AutoLigand and the use of PyRx for Virtual Screening and (4) the use of PMV and ADT for advanced visualization and structure analysis.

Each session includes lectures and hands on exercises. Students are welcome to bring their own project files for assistance during all the sessions.

Projected Outcome By the end of the sessions, the participants should be able to set up and analyze virtual screening experiments using a cluster environment. They will also be exposed to new tools including Raccoon, Fox and PyRx for the drug design and discovery process.

Instructors: David Goodsell, Ph.D., Michel Sanner, Ph.D., Stefano Forli, Ph.D., Ruth Huey, Ph.D., Sargis Dallakyan, Ph.D., Alex L. Perryman, Ph.D.

Time M-Th, 2:00 pm to 5:00 pm, Aug 1-5, 2011

Location TSRI Training Building, Room 315, Building 3377

Shuttle_Schedule From Calit2 Voigt Dr., side entrance to TSRI: 3377 N. Torreypines Ct, Room 315

  • Leave calit2 1:45 pm, arrive at TSRI 2:00 pm
  • Leave TSRI 5:35 pm, arrive at ERC conference center at 5:50 pm.

Prerequisite Basic knowledge of structural biochemistry, cheminformatics and thermodynamics is a plus. All students are required to install the prerequisite software on their own laptop prior to the session, and are encouraged to bring their own problems for assistance and discussion.


  • Monday: Basic Docking Methods with AutoDock4, Vina and ADT
    Instructors: David Goodsell, Ph.D., Ruth Huey, Ph.D.
    AutoDockTools, a graphical user interface to AutoDock, leads the user through the preparation of input files, helps to launch AutoGrid and AutoDock, and provides tools for visualizing and analyzing the results. AutoDockTools, or "adt", consists of five modules which build on the Python Molecular Viewer, "pmv". This tutorial will provide an introduction to the science of docking and an overview of AutoDockTools. Attendees will get a chance to use AutoDock hands-on and will learn how to set up, run and analyze an actual docking calculation. Also of interest to chemists interested in drug design, we will show how to visualize atomic affinity grid maps and how these may be used to design better inhibitors based on prior dockings and crystal structures.
    Tutorial Files: tutorial.tar.gz
  • Tuesday: Advanced Visualization with PMV and ADT
    Instructor: Michel Sanner, Ph.D.
    PMV (Python Molecular Viewer) is an advanced molecular visualization software that is fully integrated with AutoDockTools, and provides state of the art visualization capability for studying ligand protein interactions. Students will learn advanced visualization techniques including use of the DeJavu viewer, volume rendering, and generation of high quality graphics for publication use.
  • Wednesday: Virtual Screening with Raccoon and Fox
    Instructor: Stefano Forli, Ph.D., Alex L. Perryman, Ph.D.
    Raccoon is a graphical interface for automating the preparation of input for Virtual Screening calculations with AutoDock. Its capabilities include splitting, converting and filtering different ligand library file formats. Raccoon supports the preparation of Virtual Screening input for single workstations (Linux, Mac and Windows) and for PBS Linux clusters.
    Fox enables scientists to filter Virtual Screening results to identify compounds of greatest interest and to visualize the interactions of these compounds with the target. Fox includes a user-friendly interface to the powerful molecular visualization capabilities of the Python Molecular Viewer (PMV).
  • Thursday: Virtual Screening with PyRx and Binding Site Prediction with AutoLigand
    Instructors: David S. Goodsell, Ph.D., Sargis Dallakyan, Ph.D.
    AutoLigand uses an effective method to scan for high affinity binding pockets and reports the optimal volume, shape and best atom types for the identified ligand binding sites. It can also be used as a rational drug design tool by overlaying drug candidates on the generated fill volumes and modifying the drug to make the best use of the mapped affinity.
    During the second part of this this tutorial we'll be using PyRx to compare virtual screening result with Bioassays. We'll start by importing a sample precomputed docking result to see what to expect from a single docking experiment. Then we'll create input pdbqt files that will be used to compare virtual screening results with Bioassays. At the end of this tutorial you'll have hands-on experience on working with Bioassay data and you'll be able to run virtual screening experiments using PyRx. We'll conclude with a discussion about current limitations and advantages of virtual screening tools as well as publicly available Bioassay data.

Related Tracks from Previous SI

SI2010 Virtual Screening and Computer Aided Drug Design

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