[gmx-users] Ki estimation
r.friedman at bioc.uzh.ch
Tue Mar 11 10:10:00 CET 2008
Unless you have multiple events of binding and unbinding you cannot
directly calculate the Ki from EM or MD. You can use approximated
methods, e.g. LIE and MM/PBSA (with MD) or LIECE (for a static
structure). All of these depend on the choice of empirical parameters.
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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