Data Retrieval and Storage
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Latest revision as of 02:22, 30 October 2008
Home | The Team | The Project | Notebook |
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Evolutionary Algorithm | Data Retrieval | Modeling | Graphical User Interface |
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Contents |
Perl
- If it is an enzyme, what reactions does it catalyze?
- If it is a molecule, what is its molecular structure, and what are the synonyms for the molecule name?
UniProt
ChemSpider
The reagents from the reaction that the protein catalyzes are put through ChemSpider. This large database is much like UniProt except that it is for chemistry. Searching and querying in ChemSpider is simple because molecules can be queried using synonyms. After a molecule is queried, ChemSpider produces information about the molecule such as its SMILES, which is a simplified molecular input line entry specification. As useful as this information can be, we needed something that is machine-readable and that could be used for comparisons of metabolic pathways. What is this machine readable format? It is known as the IUPAC International Chemical Identifier (InChI). This InChi is a unique "fingerprint" of the molecule that is not ambiguous like SMILES and is supplied only by IUPAC. An example of an InChi would look like this:
1/C6H8O6/c7-1-2(8)5-3(9)4(10)6(11)12-5/h2,5,7-8,10-11H,1H2/t2-,5+/m0/s1
To see this database, visit: [http://www.chemspider.com ChemSpider]
The Algorithm
Evolutionary Algorithm | Data Retrieval | Modeling | Graphical User Interface |
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Home | The Team | The Project | Notebook |
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