Software for stability of secondary structure

Andrew Dalke dalke at bioreason.com
Thu Oct 22 20:03:57 EST 1998


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>

If there is an organization of any sort to the location of
the many secondary structure prediction programs available on
the web, I'll be astonished.  It's even worse than the number
of molecular visualization or surface calculation programs :)

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.

Since I'm already here, I did a quick web search on AltaVista.
Perhaps relevant (but no online server) is
  http://lipid.biocomp.unibo.it/piero/DG/index.html

and I haven't looked at:
> ToPLign: http://cartan.gmd.de/ToPLign.html
> ToPLign implements standard pairwise and multiple alignment
> methods with flexible parameter handling. The analysis of
> alignments is supported by offering different visualisations
> of alignments. Furthermore, the stability of the resulting
> alignments can be explored. 

						Andrew Dalke
						dalke at bioreason.com




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