[gmx-users] RE: Drug-Receptor Affinity!

Spiwok Vojtech Vojtech.Spiwok at vscht.cz
Fri Dec 5 09:37:01 CET 2003

>Dear All,
>Can we find out the affinity of a particular drug towards its receptor by 
>using any of gromacs programs.
>Many thanks in advance.
>Regards, Blaise M. Costa

If you have a clear idea on binding mode of ligand, than recent discusion
"Docking Energy confirmation" started by Filipe Maia might help you. If
you don't now a binding mode than look for some docking programs eg.
AutoDock, Dock, Slide, Glide($), FlexX($)...

Vojtech Spiwok
ICT Prague

"Docking Energy confirmation":

>>>I'm doing docking "calculations" with Autodock3.05.
>>>My question is, is there any way to use the energy minimization
>>>procedure from
>>>Gromacs to relax the conformations obtained from autodock and have
>>>a better estimate
>>>of their energy (in comparision tothe energy that autodock gives
>>>as result)?
>> If you prefer accuracy over throughput then Prodrug/gromacs minimization
>> and dynamics could be a choice. Autodock uses its scoring function
>> which includes force-field terms and empiricaly derived terms for solvent
>> effect and conformational entropy of ligand. Therefore only force-field
>> energy itself (either from gromacs or autodock) can hardly be a better
>> for scoring of ligands. You might try free energy calculation by linear
>> interaction energy (g_lie of gromacs).
>In my experience, the LIE method (rougly implemented in g_lie), gives the
>better estimate than the scoring function values from a docking program
>like Autodock, IMHO mainly because entropic factors are taken into accoount
>at least to some extent in LIE.
>What I've also done is use docked conformations as starting points for MD,
>and then cluster the resulting trajectories. It all depends very much
>on the type of system you are looking at, e.g. the behaviour of the ligand,
>the type of binding, the amount of internal degrees of freedom in the
>the flexibility of the protein (and I'm sure anyone could think of a few
>more caveats!).
>Best way, IMHO, is to try it for your particular system and if possible
>compare with experiment to determine the best performing method for you.

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