I have used this website on cell signaling website in the past to look at protein modifications.  Maybe it could help to predict dimerization.  Good luck

http://www.phosphosite.org/homeAction.do

Hi there,

Prediction is just a guess... There is nothing like experiment to state on protein oligomerization level (size exclusion chromatography is the easiest technique if you have pure protein in hand).

Thanks Brandon for the website I will try it.

Hi Dominique, guessing depending on what?? I dont know if you can just say if a protein is a dimer or monomer just by guessing and depending on nothing. specially if your proteins are novel. size exclusion chromatography is one way to go but if you dont have a pure protein you can run it in a blue native gel under non denaturing and non reducing conditions and comapre it with samples run in SDS-PAGE under reducing and denaturing conditions. 

If you have the sequence of your protein I recommend you to run protein blast and check the nature of the most similar protein, whether it is monomer or oligomer.

On the other hand you can check the domains and signature motifs in your protein and from that you can predict whether your protein is monomer or not...

All the best.

Salim, I do agree: as you say, what you want is experimental data on the oligomerization state of your protein, not the prediction mentioned in the question...

I-TASSER

Salim Al Hajri , Could you please give me some advice on native gel expriment.. iN MY LAB, there is not sufficient materials for blue native. But I can not run native successfully two.

@Ya Wan

You can run what is called a semi native gel if your target is to know if your protein forms oligomers or not. You can run your sample with out denaturing or breaking the bonds in a normal gel