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On Monday 25 April 2005 10:14 pm, Howard Salis wrote:
> I think the idea of 'modifiers' is too vague to be useful.

I think the discussions in this list are starting to convince me that anyone
who wants to be doing any modeling of biochemical systems should first have
to pass an "Enzyme Kinetics" course. The concept of modifier is not vague
at all, it is quite well defined. It seems to me that there are a number of
people out there that want to define this concept according to whatever
their software thinks a modifier is.

Power-law models do not distinguish between substrates, products or
modifiers. For power laws everything is an effector (hey, there's another
word that I expect will have a long discussion too).

As someone else already stated in this thread, a modifier is not changed by
the reaction therefore the only number that could be attributed to its
stoichiometry is zero.

Also, reactions do not need any modifier (eg activator) to proceed. If you
put NADH in contact with oxygen, it is only a matter of time that you end
up with NADP+ and water - no enzymes required.

Anyway, I am one of the defenders that software should be sufficiently
user-friendly to allow non-speciallists to carry out simulation. But this
has always meant to me that they do not need to be speciallists in
mathematics, numerical analysis, or software engineering. They DO need to
know biochemistry if they want to model biochemical systems - I'm sorry for
this lengthy rant, but I am strongly opposed that we should bastardize
terms that are objective and quite specific (and old) just because some
software happens to use them in some wrong way.
--
Pedro Mendes
Research Associate Professor
Virginia Bioinformatics Institute,
Virginia Tech, Washington St.,
Blacksburg, VA 24061-0477, USA
http://mendes.vbi.vt.edu fax:+1-540-231-2606