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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