Irwin:workshop1
This is the detailed information for workshop #1, virtual screening using two methods, by Irwin
Aim
The aim of this workshop is learn about two virtual screening approaches for discovering possible new ligands. We will use the Beta-2 adrenergic receptor. Part 1 focuses on structure-based virtual screening, using DOCK and ZINC. Part 2 focuses on ligand-based virtual screening, using SEA.
Your mission is to pick compounds you think are worth testing experimentally from among the top scoring ligands, based on pharmacological and biophysical principles that you may already know and that we will discuss with you.
Both methods are suitable for using on your own protein, providing you have a target structure (for docking) or ligand structure (for SEA). Please contact John Irwin, Rafaela Ferriera, or Brian Shoichet from the lab at this meeting, who can tell you more about molecular docking and virtual screening.
Suitability
This workshop is suitable for complete novices. If you are an expert, we suggest you not attend the hands-on session, but you are welcome to come to the "watch me" session. Also, if you want to work on your own target, please contact John Irwin or Brian Shoichet for conversation during the meeting.
Materials
All you need to do this workshop is a fairly modern browser on a fairly modern computer. It will work on Linux, Windows, and Mac. You may use PyMOL, Chimera or any other 3D molecular visualization tool for looking at the docking hits. The website for SEA is http://sea.docking.org/. Specific files for this workshop may be found at http://workshop.docking.org/erice/. The workshop makes use of results produced by DOCK Blaster and ZINC8, but these two sites will not be used directly during the workshop.
Reading Materials
These are described in the handout for the workshop, available from http://workshop.docking.org/erice/.
Protocol
Please see the files in http://workshop.docking.org/erice/ for more information. If you cannot attend the workshop, you may download these files and work through the workshop yourself. You may discuss with John Irwin or Brian Shoichet during the meeting.
Extras
There is not enough time during the two hours of this workshop to adequately treat the entire topic of docking, or ligand similarity based chemical informatics methods. We have therefore chosen to focus on interpreting the results of two kinds of virtual screens.
You are welcome, however, to use either or both of the methods used for this workshop for your own target. If you like, please give them a try, and then perhaps contact us to discuss how they worked for you.
To use SEA, please browse to http://sea.docking.org. You will need to have your actives in SMILES format, which can be created using the Java Molecular Editor, for instance, at http://jme.docking.org.
To use DOCK Blaster, a free web-based interface to DOCK, please browse to http://blaster.docking.org and/or contact John Irwin. You will need a model of your target in PDB format. More information about preparing files for docking may be found here.
-- John Irwin, March 31, 2010.