protease cleavage site program

Kresten kresten at my-deja.com
Tue Oct 26 08:56:44 EST 1999


In article <01683d2c.1f55781b at usw-ex0110-073.remarq.com>,
  nibelung <mancusoNOmaSPAM at molecool.wustl.edu.invalid> wrote:
> does anyone know of a free web program that will predict
> protease cleavage sites of a protein? thanks

The following web-sites will list you proteolytic fragments of an
entered sequence:
http://delphi.phys.univ-tours.fr/Prolysis/cutter.html
http://www.expasy.ch/tools/peptide-mass.html
http://prospector.ucsf.edu/ucsfhtml3.2/msdigest.htm

They all have different features so check them all out. One thing that
they do have in common is that none of them can tell you whether a given
site is exposed for proteolytic cleavage. So unless your protein is
unfolded you could easily miss some (all) of the predicted fragments.

At:
http://www.biologie.uni-freiburg.de/data/schaefer/lhennig/winpep.html

you can download the program WinPep which can also be used for
predicting proteolytic fragments. One advantage for this program is that
it allows you to enter own (new) protease cleavage sites.

HTH
Kresten


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