If you know the protein structure but don't know where the modulating compounds are binding, you could try out our method to predict the location of the allosteric site:

http://bioinf.uab.cat/pars

Beyond that, there are many things you can try, but to properly characterize an allosteric protein you will need to perform wet-lab experiments (mutagenesis, etc).

Hope that helps,

A.Panjkovich

Hi Yassine KASMI

If you know the allosteric site on the protein structure than you can use that information and perform docking and check the effect of it, further you can simulate the obtained conformation. But you will have to perform wet-lab experimentation to finalize or conclude your work.

Danish J

Thank you for your answers