ADL: Error in binding energy calculations

Chinh Su Tran To chinh.sutranto at gmail.com
Thu Apr 2 06:04:17 PDT 2009


hi,

I think this value -70,000,000 is not acceptable. Maybe it is a false
positive binding.
But you got other conformations with -5 to -10. They are possible ok for
these.

regards.

2009/4/2 Mostafa El Miligy <melmiligy4m at hotmail.com>

>
> Hi
>
>
>
> I used Autodock-4 for blind docking inside Trypanosoma Cruzi Trypanothione
> Reductase (PDB 1AOG) and Telomerase reverse transcriptase (PDB 3DU6) enzymes
> and some of the docked compounds showed estimated free energy of binding
> more than -70000000 Kcal/mole for the first 4 ranked conformers so is it a
> logic or acceptable calculation or not ? and if it is acceptable what is the
> explanation of this very low energy ?. However, the 5th conformer showed
> binding energy in a normal range around -5 to -10 Kcal/mole.
>
> Please reply to me as soon as possible.
>
>
>
> Thank you
>
>
>
> Yours,
>
> Mostafa El-Miligy
>
>
>
> Dr. Mostafa El-Miligy
>
> Ph.D. Pharmaceutical Chemistry
>
> Faculty of Pharmacy
>
> University of Alexandria
>
> Egypt
>
>
>
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