SI2009 Virtual Screening and Computer Aided Drug Design

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General Information

The track is geared towards beginning to intermediate level users of AutoDock in developing inhibitors for proteins, or other validated pharmaceutical targets. Those interested in cheminformatics approaches in the postprocessing 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 5. Users wishing to use a graphical user interface should also consider Track 2, where workflow tools for virtual screening will be introduced.

Participants will learn how to set up AutoDock 4 and AutoDock Vina based dockings and virtual screening experiments using AutoDockTools, and the use of the Relaxed Complex Scheme to fully account for receptor flexibilities. Additional new tools such as AutoLigand and AutoDock MMPBSA will also be introduced as a growing suite of tools for computer aided drug discovery. Advanced users are encouraged to exchange ideas with the instructors ahead of time. If you want a particular problem or topic discussed, please e-mail the instructors in advance. We will focus on the most frequent and/or most interesting requests.

Each session includes lectures and hands on exercises.

Projected Outcome By the end of the sessions, the participants should be able to set up virtual screening experiments using a cluster environment. Users will learn to use molecular dynamics techniques to develop an understanding of the relaxed complex scheme scheme and how it’s used in rescoring of AutoDock hits. They will also be exposed to new tools including Raccoon, PyRx and AutoLigand for the drug design and discovery process.

Instructors: Rommie Amaro, Ph.D., Sargis Dallakyan, Ph.D., Stefano Forli, Ph.D., Rodney Harris, Ph.D, Ruth Huey, Ph.D., Alex Perryman, Ph.D., Oleg Trott, Ph.D., Dong Xu, Ph.D.

Time M-F, 2:30 pm to 5:30 pm, Aug 3-7, 2009

Location TSRI Training Lab

Prerequisite Familiarity with the Unix environment is required. Basic knowledge of structural biochemistry, cheminformatics and thermodynamics is a plus. Familiarity with molecular dynamics theory and applications such as NAMD, and with visualization programs such as PMV or VMD is extremely beneficial.


  • Monday, Using AutoDock 4 and AutoDock Vina with AutoDockTools
    Instructor: Ruth Huey, Ph.D., Oleg Trott, Ph.D.
  • Tuesday, Using AutoDock for Virtual Screening with Raccoon and PyRx
    Instructor: Stefano Forli, Ph.D., Sargis Dallakyan, Ph.D.
    During the second part of this session you'll learn about PyRx. Please visit PyRx Website to download PyRx and watch Screencasts. PyRx is installed on all computers (18 Intel-based Macs) in the training room. Please install PyRx on your laptop if you are planing to use your own laptop. The outline is available in Getting Started with PyRx.
  • Friday, Case studies, docking flexible rings and covalent docking, Off Target Analysis
    Instructor: Alex Perryman, Ph.D., Stefano Forli, Ph.D., Rodney Harris, Ph.D.
    Students are welcome to bring their own project files for assistance during this session.

Related Tracks from Previous SI

SI2008 Virtual Screening and Computer Aided Drug Design

Back to SI2009 program

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