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Hiro,


>So basically, what you are saying is that I cannot use Shea-Acker's model
>to show why sometimes modifiers need stoichiometries because Shea-Acker's
>model is a dangerous one?
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>
>
No I said that it is dangerous, as it barely fits into the biochemical
paradigm, and if you throw in some spice (like folds, mutations etc,
things that have combinatorial and physical effects) BP will not be able
to model it.
THEN I said how I would model it. So I did not invalidate your example.
You are wellcome to present it as a use case.

I've just checked the original paper, and I can not understand where
modifier stochiometry comes into play in Shea-Ackers model. It very Can
you eloborate on that?

>People use this type of abstraction. At least Phage lambda, type 1 pili
>in E coli., b-subtilis have been modeled using this type of abstraction.
>And I don't think it's dangerous, and in fact it will generate a good
>approximation as long as rapid equilibrium assumption holds (and that's
>usually the case for operator site binding).
>
>
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Can you also pls be kind enough to give pointers for these models, so
that we can have a more solid ground?

>Yes, it could have 4 configurations as you described, although that's not
>the point I was trying to make. If all 4 configurations can lead to open
>complex formation, then you should have 4 reactions. If you don't have
>modifiers, then the only configuration you can be in is nothing bound to
>operators. The propensities of the other 3 configurations should be 0.
>
>
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Perhaps you missed it but what happens if you have three promoter sites?
Also please note that these sites are different with different binding
constants, different ( and sometimes cancelling) effects. How do you
counter the fact that substrate/product stochiometry is a constant, as
opposed to variable modifier participation? Actually how do you oppose,
Pedro Mendes' point?

>I don't understand what you mean by "better system." If you can simulate
>and analyze the system using this type of model without using a
>supercomputer, shouldn't this be better for those who don't have access to
>supercomputers?
>
>
When I say a better system, I am not in any way mentioning about
computational completeness or such. But I am talking about carefully
controlled ambigouity and incompleteness. We do not know everything, (
and even if we do, I think we would still have a lot of problems), but
it is a shame if you loose something you already know while modeling,
because your ontology captures it ambigously.

Best,
Emek