[EMBOSS] Algorithms for pI and molecular weight in pepstats

[Jake Rothenbuhler]

Thanks to Ingo and Peter for the quick and helpful replies. I've read
through the discussion you had a year ago on this topic and it seems
like it is still unresolved.

> The isoelectric point can be calculated for various conditions. When I

> checked last, ExPASy's protparam was set up the isoelectric focus
phase 
> of 2D gels under high urea conditions. It was unclear at the time
where 
> to find all the values needed to reproduce their calculation.

I have been reading through the literature referenced by ExPASy's
documentation. The article does not give pK values for all N-terminal
residues. I've asked ExPASy support about the pK values used for
residues not listed in the paper. If you're interested, I can keep you
updated regarding their response.
 
> We would like to update EMBOSS's protein property calculations,
possibly 
> with additional options or alternative parameter sets.

If it's something you'd like to include in EMBOSS, I'd be willing to
contribute to an additional option for pI calculation that uses ExPASy's
pK values.

Jake Rothenbuhler
Bioinformatics Programmer/Analyst
XOMA (US) LLC
(510) 204-7452

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