SI2008 Virtual Screening and Computer Aided Drug Design
This track will cover the Relaxed Complex Scheme using Molecular Dynamics Simulations and virtual screening using AutoDock and AutoDockTools.
Time: 1 pm to 5 pm
Location: PFBH 161
- Tuesday, Aug 5, Using AutoDock with AutoDockTools
- Instructor: David Goodsell, Ruth Huey
- Users will learn how to use ADT to set up docking experiments, basics in parameter optimization, and an introduction to the use of Opal-based web services for docking analysis.
- AutoDock4 Tutorial
- Wednsday, Aug 6, Using AutoDock for Virtual Screening
- Instructor: Ruth Huey, David Goodsell, Alex Perryman
- Users will learn how to set up large scale virtual screening experiments using AutoDock through a well established tutorial. The use of Vision and Opal based web service for large scale virtual screening will be introduced.
- Virtual Screening
- Thursday, Aug 7, Relaxed Complex Scheme
- Instructor: Dong Xu, Rommie Amaro
- Users will be introduced to the use of molecular dynamics to fully account for receptor flexibility, and how to use clustering algorithms to capture the representative snapshots.
- Relaxed Complex Scheme, Part I: Molecular Dynamics and Clustering
- Friday, Aug 8, Relaxed Complex Scheme
- Instructor: Rommie Amaro, Dong Xu, Alex Perryman
- Users will be introduced to the use of the relaxed complex scheme (RCS), redocking and rescoring of AutoDock hits.
- Relaxed Complex Scheme general: Virtual Screening and RCS Rescoring
- Relaxed Complex Scheme, Part II: Virtual Screening and RCS Rescoring