ADL: Needed your suggestion........

Nicolas Sapay nicolas.sapay at cermav.cnrs.fr
Tue Mar 30 02:28:39 PDT 2010



ratnakar mandla a écrit :
> Hii Users,
>  I have a questions to all of you please help me in understanding this
> topic.
>
> What is desolvation energy? How can desolvation energy of ligand molecule
> affect its binding energy towards a receptor.
>   
In vivo, the ligand and the receptor are bathed in water. To interact, a 
part of the water solvating the ligand and the binding site need to be 
removed. If both are polar, this will probably cost some energy. In 
molecular docking, water molecules are not explicitly represented, 
although they appear indirectly through the way the desolvation energy 
is calculated.
> What is the entropy upon ligand binding  in (interior side of the protein) &
> ligand binding on exterior side(surface) of protein.
>   
The concept of entropy is certainly hard to deeply understand. To keep 
it simple, it is related to the number of conformations your ligand and 
your receptor may adopt in the free state compare to the bound state. 
Normally, the bound state limits this number and this cost entropy. This 
is not necessarily related to exterior vs interior of the protein 
(although one would expect it cost more to bind a compound in a pocket 
than on a surface). It rather depends on the flexibility of your ligand 
and your binding site and this flexibility is affected after binding. In 
Autodock 4, the entropy penalty is directly calculated from the number 
of degrees of freedom of your ligand (IIRC).

Cheers,
Nicolas
>
> Thanks for your help
>
> Thanks
> Ratna
> ________________________________________________
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>
>   
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