[gmx-users] Ki estimation

Maik Goette mgoette at mpi-bpc.mpg.de
Tue Mar 11 12:36:34 CET 2008

You can't compare a Ki directly from the MD AFAIK.
What you could do is, computing the free energy difference between two 
ligands and compare it to the difference in Ki (which actually is 
closely related to the famous Kd), if that helps you


Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/

V. Tanchuk wrote:
> Dear Users,
>     I am working Drug – Enzyme Complex. Unfortunately, docking software 
> (AutoDock) was not able to give any resonable results. I have tried to 
> use Gromacs and got a resonable binding. The best results were obtained 
> in the case of simple minimization of the crude AutoDock's results. The 
> question is how to estimate Ki.
>     There is also another problem. I have the best correlation between 
> experimental and calculated results only for the total energy in the 
> case of optimization (it seems that other kids of energy are not 
> available without molecular dynamics, but total or any other energies 
> obtained after molecular dynamics do not correlate).
> Thank you in advance for your help.
> Sincerely yours,
> V. Tanchuk
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