[gmx-users] Estimations of the drug's affinity

Justin Lemkul jalemkul at vt.edu
Sun Apr 14 13:24:18 CEST 2013

On 4/14/13 2:13 AM, James Starlight wrote:
> Dear Gromacs users!
> I wounder to know if it possible to simple estimate drug affinity by mean
> of MD simulation? As I know the drug's property is based on the free energy
> change of bound-unbound ligand. So It seems that Justin's tutorial (free
> energy calculations) might be usefull if it would not be so routine for the
> drugs ( in that workflow several coulombic-vdw interactions must be
> uncoupled). Is there any more easily way to perform such calculations for
> the typical small-drug compounds consisted of several non-covalent
> interactions with the receptors ?

Free energy calculations require considerable effort.  You can approach the task 
in a number of ways - FEP, BAR, TI, LIE, PMF, MM/PBSA, etc.  There is a large 
body of literature detailing methods for such calculations.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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