[Dock-fans] Fwd: Model of lipid bilayer for docking

[Francesco Pietra]

I am posting again because on the Chimera list - in the context of a related
question - I was advised to possibly strip out the lipid bilayer before going
to Dock from Amber.

Though, I have seen recently a docking study (GOLD 3.0) with a membrane
protein, where the authors carefully immersed the protein in a thick layer of
octane and then the whole was solvated with water.

I would be grateful for advice about.

Thanks
francesco

--- Francesco Pietra <chiendarret at yahoo.com> wrote:

> Date: Thu, 11 Oct 2007 22:45:17 -0700 (PDT)
> From: Francesco Pietra <chiendarret at yahoo.com>
> Subject: Model of lipid bilayer for docking
> To: dock-fans <dock-fans at docking.org>
> 
> I have raised a discussion on the tools available for building lipid
> bilayers.
> 
> In that context I suppose that phosphatidylcholine- or
> polyenylphosphatidylcholine-based bilayers are computationally very costly.
> Under the presumption that octane-water models of  lipid bilayer involve much
> less computational cost, are they a promising initial route in the
> exploration
> if there is any docking at all with complicated - non polymeric - potential
> ligands? Also, are there examples of docking using more advanced models of
> lipid bilayer?
> 
> Separately I have asked is complex bilayers built with VMD are transferable
> to
> the Amber-Dock-Chimera world.
> 
> Thanks
> francesco pietra 
> 
> 
>        
>
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