Track 5: Virtual Screening using AutoDock Tools

Virtual screening is a critical technique in the drug discovery process. It enables the rapid screening of a large number of compounds in libraries against a known macromolecular target to identify leads for further optimization. AutoDock is one of the most cited docking software in virtual screening.

Goal: 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 master new tools including Raccoon, Fox and PyRx for the drug design and discovery process.

Target Audience: 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 also consider the molecular electrostatics and diffusion track. Those interested in the use of molecular dynamics techniques in ensemble based virtual screening should also consider the CADD track.

Prerequisites: 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.

Topics: Basic Docking Methods with AutoDock4, Vina and ADT; Advanced Visualization with PMV and ADT; Virtual Screening with Raccoon and Fox; Virtual Screening with PyRx and Binding Site Prediction with AutoLigand

Format: Presentations and hands-on tutorials.

Course Materials

Location:
  • Computational Biology Building, Room 315,
    3377 N Torrey Pines Court, La Jolla, CA 92037
Time:
  • 14:00 - 17:00, M-Th  July 30 - August 2
David Goodsell, Ph.D.
Ruth Huey, Ph.D.
Michel Sanner, Ph.D.
Stefano Forli, Ph.D.
Alex L. Perryman, Ph.D.