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Inhibitors against membrane-bound proteins

PostPosted: Mon Jan 11, 2016 8:32 pm
by sreiling
Sargis! Greetings!

I have a membrane bound protein, whose structure has yet to be solved, for which I'd like to test inhibitors against. I will obtain a hypothetical structure using Phyre 2, and from there, I'd like to do the in silico testing using PyRx.

Is there any way to model a simple lipid bilayer in PyRx, such that the transmembrane regions are within it? I don't want the tested inhibitors to bind to those regions (since that would be unrealistic in vivo or in vitro).

Re: Inhibitors against membrane-bound proteins

PostPosted: Tue Jan 12, 2016 2:23 am
by sargis
Greetings Scott!

I haven't thought about modeling a simple lipid bilayer in PyRx. I would interested to know what would be a good user interface for that. You can limit the grid box to the region of interest if you want the ligand to bind to a particular region. I'm always interested to hear about new features that would make PyRx more useful.