Proteolytic map, freeware or web site?

[Uncle S]

> Zeev Pancer wrote:
> > Can anyone refer me to a freeeware or web site that can search a protein
> > sequence for clevage-sites of proteolytic enzymes?

Mathew Woodwark wrote: 
> You might like to try ms-digest in proteinprospector. It is part of a
> package that using mass spec peptide mass data t identify proteins and one
> of the programs allows you to paste in a sequence and have it cut by a
> number of proteolytic enzymes
> 
> The address is
> 
> http://prospector.ucsf.edu/

An excellent suggestion.  If you're going to do a lot of digestion
simulations, you might not want to do it all over the net.  PAWS is a
really handy mass spec program that you can put on a Wintel or Mac
machine.  Prospector is nice for chopping up proteins that you pull out
of databases, but I do most of my mass spec work with PAWS.

here's the site
http://www.proteometrics.com/

be warned, it runs on java, so turn that language on in your browser.

better yet, use one of the alternate pages:

http://www.proteometrics.com/version2.html

http://www.proteometrics.com/version1.html
(bare bones)


Shamus