I am trying to calculate the binding constant of drug after docking through Auotdock4. Can anyone tell me what value of Temperature should be taken during the calculation? It has also been know that Genetic algorithm used during docking is independent of Temperature. So, Is it right to calculate binding constant after docking? Please suggest some appropriate answers.
Hi Ishrat Jahan In the dlg file it appears as:
DOCKED: USER Estimated Inhibition Constant, Ki = 8.03 nM (nanomolar) [Temperature = 298.15 K].
For more information consult this article: Article Computational protein-ligand docking and virtual drug screen...
Best wishes
Can anyone tell me, is it possible to dock same (one) ligand in multiple quantities simultaneously?
Either 300 or 298 K can't affect your results - in docking simulations you apply lots of assumptions, so don't be worry about this issue. Docking simulation is a tool to place a ligand inside the ligand-binding domain with many approximations and its score is not worth evaluating in most cases - it gives you an initial idea about the probable ligand position.
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