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substrate for kinase - finding the predicted substrate for a kinase (Aug/17/2010 )

Hi, does anybody know a free program that predicts the possible substrates for a kinase?
Also, does anybody have experience with protoarray (KSI) from Invitrogen, is it any good?

Thanks in advance
Charline

-Charline-

Charline on Wed Aug 18 06:50:48 2010 said:


Hi, does anybody know a free program that predicts the possible substrates for a kinase?
Also, does anybody have experience with protoarray (KSI) from Invitrogen, is it any good?

Thanks in advance
Charline


well, you can predict sites for known kinases within a given protein (I dont know by heart the sites, but if you check in google with prediction phosphorylation or something like that you will find some places). You can check as well phosphosite.org to find the sites in a given substrate

-laurequillo-

laurequillo on Wed Aug 18 07:28:09 2010 said:


Charline on Wed Aug 18 06:50:48 2010 said:


Hi, does anybody know a free program that predicts the possible substrates for a kinase?
Also, does anybody have experience with protoarray (KSI) from Invitrogen, is it any good?

Thanks in advance
Charline


well, you can predict sites for known kinases within a given protein (I dont know by heart the sites, but if you check in google with prediction phosphorylation or something like that you will find some places). You can check as well phosphosite.org to find the sites in a given substrate


Thanks, I have found several programs for predicting the phosphorylation sites on my kinase, but how do I find the potential substrates that can be phosphorylated by my kinase?

-Charline-

Charline on Wed Aug 18 07:59:54 2010 said:


laurequillo on Wed Aug 18 07:28:09 2010 said:


Charline on Wed Aug 18 06:50:48 2010 said:


Hi, does anybody know a free program that predicts the possible substrates for a kinase?
Also, does anybody have experience with protoarray (KSI) from Invitrogen, is it any good?

Thanks in advance
Charline


well, you can predict sites for known kinases within a given protein (I dont know by heart the sites, but if you check in google with prediction phosphorylation or something like that you will find some places). You can check as well phosphosite.org to find the sites in a given substrate


Thanks, I have found several programs for predicting the phosphorylation sites on my kinase, but how do I find the potential substrates that can be phosphorylated by my kinase?


Well, I never used such a program...is quite a wide search dont you think? maybe there are some programs for that, but it would be easier if you have some target protein which you want to know if it is phosphorylated by your kianse. Then the programs will give you some predicted sites. But fo some kinases those conserved motif are quite open, so in a protein you could have several "predicted" sites, but it doesnt mean that your kinase is gonna phosphorylate those sites for sure...
I dont know if it helps you

-laurequillo-

Here's another alternative for kinase profiling: http://www.pepscanpresto.com/index.php?id=27 (PepChip). I am going to try their trial slide, which has 200 known kinase targets, and is not really expensive...
Disadvantage: If you need a scaffold or linker protein for your kinase action (like for all the MAP kinases), it won't work. Then I'd recommend something like fishing phosphorylated proteins after kinase treatment of a crude dephosphorylated cellular extract. There you'll get the consensus kinase target sequence.


Cheers,
Rsm

-Minna-

Rsm on Wed Aug 18 10:26:37 2010 said:


Here's another alternative for kinase profiling: http://www.pepscanpresto.com/index.php?id=27 (PepChip). I am going to try their trial slide, which has 200 known kinase targets, and is not really expensive...
Disadvantage: If you need a scaffold or linker protein for your kinase action (like for all the MAP kinases), it won't work. Then I'd recommend something like fishing phosphorylated proteins after kinase treatment of a crude dephosphorylated cellular extract. There you'll get the consensus kinase target sequence.


Cheers,
Rsm


Thanks!!!

-Charline-

For the kinase substrate you can use PlosOne as a program it may help you and i dont have any experience with protoarray but it seems ok for your work.

for further queries:biology test papers

Regards
Rupam Mittal

-Rupam-