SI2011 Computer Aided Drug Discovery Pipeline

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General Information

The track is geared towards both beginning and intermediate level users of NAMD and 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.

Each session includes lectures and hands on exercises.

Projected Outcome By the end of the sessions, the participants should be able to set up MD simulation and analyze virtual screening experiments using the NBCR CADD pipeline. 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. Participants will learn the Relaxed Complex Scheme to fully account for receptor flexibilities through MD simulation and virtual screening. All the workflows have been represented using the NBCR CADD pipeline.

Instructors: Rommie Amaro, Robert Swift, Yi Wang, Cesar Oliveira, Stephen Lindert, Denis Bucher, Wilfred Li

Time M-F, 9:00 am to 12:00 pm, Aug 1-5, 2011

Location Classes will be held in the Computer Science and Engineering Building (Tu-Th Room 1202, Fr room 2154)


  • 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, VMD, or Molegro is highly recommended (but not strictly required).
  • Students are required to bring their own laptop, with CADD Pipeline and one of the visualization programs such as PMV and VMD preinstalled. The latest version of the CADD pipeline can be found in MGLTools 1.5.6
  • Students in the CADD Pipeline track are requested to work through the VMD tutorial on their own before classes start on Monday. This tutorial takes approximately 2 hrs.
  • It will be helpful if students work through the Using AutoDock4 with AutoDockTools tutorial


  • Monday: Setting up an MD simulation
    Instructors: Cesar Olivera, Ph.D., Yi Wang, Ph.D.
    Students will learn the basics of MD simulation with NAMD using neuraminidase as the experimental system. Key input files and their preparation will be introduced and basic operation of the CADD pipeline explained.
    Talk slides: MDintro1.pdf and MDintro2.pdf
  • Tuesday: Trajectory Structure Analysis using RMSD-based Clustering and QR Factorization
    Instructors: Robert Swift, Ph.D., Denis Bucher, Ph.D.
    Students will learn how to analyze trajectories for distinct receptor conformations using clustering methods such as Ptraj and QR factorization.
    CADD clustering tutorial
    CADD QR factorization tutorial
    Talk slides
  • Thursday: Visualization, Rescoring and Hit Analysis
    Instructor: Rommie Amaro, Wilfred Li, Ph.D.
    Students will learn to visualize the virtual screening results, and perform basic interaction analysis and rescoring. Students are welcome to bring their own project files for assistance during this session.
    Visualization tutorial
    Please download 0.1.1 version of the visualization workflow and place it in CADDworkflows/visualization folder. You should remove the 0.1 version of the workflow from the visualization folder.
    CADD Workflow Tutorials Collection
    Talk slides
  • Friday: New CADD Applications
    Instructor: Yi Wang, Ph.D., Denis Bucher, Ph.D., Steffen Lindert, Ph.D.
    Accelerated Molecular Dynamics (aMD) is introduced to enhance the sampling of receptor conformations through MD simulation, followed by a brief introduction to the lead optimization tool AutoClick/AutoGrow.
    Alanine Dipeptide aMD simulation
    Talk slides: Enhanced Sampling, aMD and Autogrow

Related Tracks from Previous SI

SI2010 Virtual Screening and Computer Aided Drug Design

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