ADL: BILAYERS

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ADL: BILAYERS

Gavin Seddon-2
Hello
Can anyone tell me if ad can be used for molecular docking within a
lipid bilayer environment?
THANKS
G
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Re: ADL: BILAYERS

Nicolas Sapay
Hello,

Apparently, you didn't get much answer... I'm not an Autodock wizard but
I've got some experience with lipid bilayers. The main difficulty is that
the dielectric constant depends on the position in the bilayer. As far as I
know, Autodock uses a single value as dielectric constant, which is a simple
way to model an homogeneous solvent. If you want to dock ligands in a lipid
environment, you can just modify this constant to some appropriate value and
hope for the best. Otherwise, you will have to work with more complex
implicit models of solvation. In that case, an MD simulation package
(CHARMM, Gromacs, ...) is  probably more appropriate, though not
straightforward.

Regards,
Nicolas

Gavin Seddon a ├ęcrit :

Hello
Can anyone tell me if ad can be used for molecular docking within a
lipid bilayer environment?
THANKS
G
________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---