BIOT 242 |
| Designing novel biochemical pathways is a highly subjective process. The current range of chemistries that enzymes catalyze is diverse enough that for most target molecules, there exist many possible combinations of enzymes that can theoretically synthesize the target compound. Popular enzyme databases like BRENDA, MetaCyc, and KEGG do not readily lend themselves to pathway design, because the information contained within these databases cannot be queried based on the chemical or functional group transformations that the enzymes themselves catalyze. That is, while these databases do allow users to query their contents based on static substructures, they do not allow querying for dynamic chemical changes that either create or destroy a given substructure. This type of query would be useful when identifying enzymes that create structures and compounds of interest. To address this issue, we have created ReBiT (Retro-Biosynthesis Tool), the database of enzymatic transformations, to assist synthetic biologists and metabolic engineers in designing novel pathways towards valuable target compounds. ReBiT allows a user to query molecular structures against a database of enzyme-catalyzed chemical transformations. ReBiT returns hits (enzyme-catalyzed chemical transformations) in which the queried structure changes or reacts. Selecting a particular transformation lists all three-digit enzyme classification (E.C.) numbers that contain enzymes catalyzing that transformation as well as links to the ExPASy database for more detailed enzyme-specific information. ReBiT also displays graphical representations of all structures involved in each transformation, any cofactors or co-substrates used, and additional, useful commentary (usually specific four-digit E.C. numbers catalyzing each transformation). |
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Poster Session
5:30 PM-7:30 PM, Wednesday, August 22, 2007 BCEC -- Exhibit Hall - B2, Poster
Division of Biochemical Technology |