1. Why Rxn2Bio?
Rxn2Bio is developed to automatically bridge the biosynthesis gap between biosynthesis reactions and catalytic enzymes.
2. What can I obtain from Rxn2Bio?
Using Rxn2Bio, you can get catalytic enzyme links needed for an input biosynthesis reaction.
3. How does Rxn2Bio work?
Rxn2Bio proposed a combination method of reaction similarity and reaction diversity to bridge gap between reactions and enzymes by predicting EC numbers of reactions. Reaction similarity focused on reactions with similar chemical transformation patterns. Reaction diversity considered molecular complexity of reactants and products. Reactions with similar transformation patterns are usually described by the first three digitals of EC numbers. Reaction diversity is used to predict the fourth digital of EC numbers.
4. Why EC number?
The basis of linking genomics and chemistry is the EC numbers [JACS, 2004; Enzyme Nomenclature, 2002; Bioinformatics, 2009; PLOS Comp. Bio. 2010]. The EC numbers represent enzymatic reactions (chemical information), but they are also utilized as identifiers of enzymes and enzyme genes (genomic information). The EC number plays a key role in classifying enzymatic reactions and in linking the enzyme genes or proteins to reactions in metabolic pathways. This duality of the EC numbers makes it possible to link the genomic repertoires of enzyme genes to the chemical repertoire of metabolic pathways.
5. Why reaction similarity?
In RxnFinder, our group has successfully applied reaction similarity to search biochemical reactions [Bioinformatics 2011]. Reaction similarity was developed to find reactions with similar chemical transformations.
6. Why reaction diversity?
Similar reactions are distinguished by the molecules participating in the reactions. The molecules are quantitatively measured by considered the overall molecular diversity. Here, we proposed a concept as reaction diversity to measure the overall molecular diversity. Reaction diversity is defined as the sum of molecular diversity participating in a reaction.