What Is The Best Website For Predicting Potential Protease Sites?

Question

[Bobthejoe]

I have tried PeptideCutter on ExPASy but there is just a data deluge. I was curious if there was a better resource that would provide a clearer picture.

I'm looking at an recombinant protein produced in E Coli (K12 derivative). I'm trying to figure out what is cutting my protein during the in vivo synthesis process.

[Larry_Parnell]

I think some details would help. Are you looking at eukaryotic proetins subject to bacterial cleavage? Or euk proteins treated with peptidases from that same organism? Are plants the basis of your work? What are the conditions of the peptidase activity (some work at restricted pH or temperature, eg)? In other words, can you filter the PeptideCutter results in any way, because this is often the source of choice?

Answer 1

[julieN]

I don't know if they're better, but some alternatives are:

http://merops.sanger.ac.uk/cgi-bin/show_substrate

http://cutdb.burnham.org/

http://clipserve.clip.ubc.ca/topfind

[Bobthejoe]

Unfortunately these all require knowing what protease is cleaving your protein. It's a good database though.

Answer 2

[Cdsouthan]

For de-novo prediction of candidate clipping points domain boundaries, disordered sections and surface loops are the typical guesses but we need more context Bob

[Bobthejoe]

What type of information is usually required. I guess that is the point of the question.