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 David Wishart

Talk Title:
The Bioinformatics of Small Molecules

Date/Time:
October 13, 2005, 3:30pm

Affiliation:
Department of Computing Science and Biological Sciences, University of Alberta.

Abstract:
When we think of bioinformatics we often think of its applications to large biomolecules such as DNA, RNA and proteins. However, it is important to remember that the genes and proteins in cells are all polymers of small molecules. Not only are small molecules important in the synthesis and maintenance of DNA, RNA and proteins, they are also vital to the regulation of genes, enzymes and the general cellular environment. It is little wonder, then, that 99% of all FDA approved drugs are small molecules. So clearly small molecules are important. But why are they so often left out of most bioinformatics databases and bioinformatics software tools? Why is there so little integration of small molecule (chemical) data with large molecule (gene/protein) data? In this presentation I will provide a brief overview of the recent attempts that bioinformaticians are now making to integrate chemical information (cheminformatics) with biological information (bioinformatics). I will highlight some of the newly developed databases (PubChem, BIND, KEGG) that are at least partially dedicated to small molecule/large molecule integration. I will also describe some of the work going on my lab aimed at developing several newly integrated databases including DrugBank, CytP450-Free, and the Human Metabolome Database (HMDB). Finally I will discuss efforts we are undertaking to model metabolism and small-molecule mediated events in the cell through our newly developed cellular simulation software called SimCell.

Student Presentation:
Yvonne Li, Bioinformatics Training Program for Health Research
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