fitting with dynafit?

Jim Reid j.reid at sheffield.ac.uk
Thu Aug 9 10:28:39 EST 2001


Hi,

I've cc'd this to bionet.matabolic-reg as it seems to be the closest to
a "numerical modeling in enzymology" newsgroup.  

Anyway I suppose it very much depends on what you are trying to do. 
I've fitted binding data without too many problems but that isn't very
tricky.  When I've tried to fit more demanding data sets (e.g. progress
curves at varied ligand and enzyme concs.) I've had more problems.  On
the basis of _very_ little experience (you have been warned!) these can
be due to problems analogous to determining Vmax when [S] << Km.  These
are easy to spot when an analytical equation describing the model is
available but harder when you are only dealing with progress curves. 
Perhaps a good safety net would be to simulate curves for your fitted
parameters in concentration regions that are far from your
experimentally explored ones.  This is a bit off topic now but might get
a discussion going.

As for the initial value problem, I have suffered from this when trying
to simulate the first few minutes of the time course of an enzyme with a
long lag phase in an attempt to get a steady state rate.  I am not
convinced that this is anything to do with the program (similar problems
with kin/fitsim), but that there are a lot of local minima and picking
good starting values is just essential.

Looking back over this it doesn't look very helpful but I'd also be
interested in hearing about the success stories or problems that people
are having with these numerical methods.  Are they worth the effort?
Always? Sometimes - It depends? Never, just design expts. to avoid
them?  

All the best,

Jim
 
ricnews wrote:
> 
> Hi,
> 
> I'm wondering if anyone successfully used dynafit to fit their data to a
> model? I tried but even with a simple test I couldn't get it to fit unless I
> gave it starting values that were basically the answer. Using starting
> values that converge easily in sigmaplot or excel dynafit still couldn't get
> the answer.
> 
> I received no response from the author so I was hoping someone else might
> use the software and be able to help me out.
> 
> Thanks,
> Ric




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