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

[James Starlight]

Justin,

and what exactly method from that list could be most easily performed in
gromacs for the estimation of the affinity of small mollecules to the
membrane receptors?

2013/4/14 Justin Lemkul <jalemkul at vt.edu>

>
>
> 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
>
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> ==============================**==========
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> 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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