[sbml-discuss] Representation of Co-enzymatic reactions in SBML

Pedro Mendes mendes at vt.edu
Mon Sep 20 12:14:50 PDT 2004

On most cases "Co-Enzymes" are actually substrates or products of reactions 
(eg NAD+/NADH, ATP/ADP). The other use for the word "Co-Enzyme" is for 
prosthetic groups (eg Heme, metal ions, etc). In the first case the correct 
SBML assignment is as substrate and product. In the second case it is as 
modifier (since they are definitly activators!).

I don't know what else you may mean by "Co-Enzyme" that does not fit the above 
two categories. Could you explain this further (a specific example would be 

On Monday 20 September 2004 09:21 am, Subhashni wrote:
> Hi All,
> We are developing a pathway editor tool based on the SBML level 2 specs for
> our client. The client requirement also includes representation of
> Co-enzymatic reactions. To represent the same we have decided to include a
> new set of tags.
> The new tags that will be introduced are:
>          <listOfCoEnzymes>
>            <coEnzymeSpeciesReference species="ABC"/>
>            <coEnzymeSpeciesReference species="CDE"/>
>          </listOfCoEnzymes>
> 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.
> Secondly, since the concentration of co-enzymes remains unchanged during
> the reactions, it cannot be represented as reactants
> or the products. But, if the user prefers to specify a concentration for
> the co-enzymatic reaction, it would be possible only if it is part of the
> model section. So we have introduced the new tags mentioned above.
> Warm Regards,
> Subhashni

Pedro Mendes
Research Associate Professor
Virginia Bioinformatics Institute, 
Virginia Tech, 1880 Pratt Drive
Blacksburg, VA 24061, USA
http://mendes.vbi.vt.edu     fax:+1-540-231-2891

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