Erice2008:workshop2
From DISI
This is the detailed information for workshop #2, EBI Tools.
|
Aim
The aim of this "hands on" workshop is to provide an introduction to the tools and databases available at the European Bioinformatics Institute (EBI) that can help with a structure-based ligand discovery project. We will use some real life examples to illustrate how to search the resources available, the types of information that can be retrieved and how the results can provide meaningful biological insight. As all of the resources are available from the EBI website there will be an option to analyse your own protein.
Note: If you wish to analyse your own structure please contact James Watson (watson@ebi.ac.uk) in advance of the course and no later than two weeks beforehand to ensure that the available analyses are able to be run.
In addition to this there will also be a "watch-me" session which will demonstrate the prediction of function from structure as part of a structural genomics initiative.
Suitability
This workshop is aimed at novice users, however we advise that you will be expected to have had some experience of using molecular graphics packages such as RasMol/Jmol, PyMol or AstexViewer. More challenging options for experts will be available in the handout.
Materials
All that is required to take part in this workshop is a fairly modern browser on a fairly modern computer - the latest Java runtime environment should be installed to allow many of the Java applets to run, Adobe flash player is also advised to be installed.
For the effective use of ProFunc, PDBsum and some MSD services, RasMol should be installed locally. Information on getting and installing Rasmol and setting up the browsers can be found at:
- http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?doc=TRUE&pdbcode=n/a&template=doc_viewers.html[1]
Other websites to look at before the workshop:
Protocol
In the examples chosen we will be using a variety of resources from the EBI including, but not exclusively:
- MSD resources (MSDlite, MSDsite, MSDchem, MSDmotif, MSDfold, etc.)
- ChEBI
- IntEnz
- PDBsum
- ProFunc
- Procognate
The detailed course instructions will be made available online shortly before the Erice meeting.
Extras
If you finish the workshop early you can analyse your own structure (remember to inform James Watson in advance that you would like this option), or look at one of a number of real structural genomics targets of unknown function that will be made available for analysis.
