Software for stability of secondary structure

Vladimir Svetlov svetlov at oncology.wisc.edu
Thu Oct 22 23:34:26 EST 1998

In article <362FD5FD.3B4EABB7 at bioreason.com>, Andrew Dalke
<dalke at bioreason.com> wrote:

> greg at franklin.burnham-inst.org (Dr. Greg Quinn) said:
> > Vladimir
> > I think you're being over-sensitive; the term 'littered' is
> > simply used here to mean 'frequently found', unless I've missed
> > some kind of subtext.
> To be precise, Merriam-Webster has for "littered"
> > 3 a : to strew with scattered articles b : to scatter about in
> > disorder c : to lie about in disorder <their upside-down hats
> > littered the top of the bar -- Michael Chabon> d : to mark with
> > objects scattered at random <a book littered with misprints>

Well, if Meriam Webster's saz so it must be true then. So when you see a
sign smth. like "Don't litter the highway" it simply means that the authors
want you to neatly arrange your rubbish in a non-random fashion (such as in
heaps matching in size the set of prime numbers), rather than not
obstaining from throwing away the litter... Well, you could try it and
argue with a state trooper that according to Meriam Webster's dictionary
littering has nothing to do with the kind of articles that are being
scattered but rather with the orderly or disorderly fashion of the

> To answer the original question from Rich Dudley <rdudley+ at pitt.edu>
> > Are there any measurements available that will give the
> > *stability* of the structure?
>   I know that ProParam from ExPASy
>       http://www.expasy.ch/sprot/protparam.html
> produces an "instability" index for the whole protein, but
> that's all I know.  I've never tried it and cannot vouch for
> it's usefulness.

If you were so big on dictionary-derived definitions you should know that
ProParam does not fit the category of the "measurement", the proper answer
should be then "scanning microcalorimetry".


Vladimir Svetlov, PhD
McArdle Lab for Cancer Res.
1400 University Ave.
Madison, WI 53706

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