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

[Justin Lemkul]

On 4/14/13 8:54 AM, James Starlight wrote:
> 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?
>

There is no universal answer to that question.  Explore the literature; there is 
a vast amount of information available on such calculations.  Proceed with 
whatever is feasible and most reasonable for your purposes.

-Justin

> 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
>>
>> --
>> ==============================**==========
>>
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>
>> ==============================**==========
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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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================