Forums

> "Coenzymes/Cofactors have not been provided with a separate tag under SBML
> scheme. In the model files kept in SBML Model Repository, they have been
> presented as reactants and "products" under the tag- Specie.

As far as I know, the definition of a co-enzyme is quite vague, and
depends much on the person who's considering the reaction. According to
the model, it can be put as a "reactant" or a "modifier". I can't imagine
a situation where none of these are possible.

>>It is not possible to represent the co-enzymes using the existing tags
>>available in the model section. The reason is that the co-enzymes cannot
>> be represented under the tag of modifiers because Co-enzymes are not
>> modifiers in their full sense, as they do not play a vital role in
>> inhibiting or activating a process. Rather a co-enzyme induces an
>>inhibitor or activator to act upon the reaction under consideration.

The modifier can be the complex enzyme/co-enzyme. Beside, some co-enzyme
do actually react withe the substrates.

>>Secondly, since the concentration of co-enzymes remains unchanged during
>>the reactions, it cannot be represented as reactants
>>or the products.

Well, in fact the concentration of some do. It depends how you choose to
model it. For instance you can choose to explicitely model protonated and
unprotonated versions.


--
Nicolas LE NOVÈRE, Computational Neurobiology,
EMBL-EBI, Wellcome-Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
Tel: +44(0)1223 494 521, Fax: +44(0)1223 494 468, Mob: +33(0)689218676
http://www.ebi.ac.uk/~lenov