ADL: Error in binding energy calculations

bagdevi.mishra at gmail.com bagdevi.mishra at gmail.com
Sat Apr 4 02:50:28 PDT 2009


repeat your docking protocol and see what results you get.

Regards,
Bagdevi Mishra.



On Thu, Apr 2, 2009 at 6:51 PM, Gavin Seddon <home at gavsed.net> wrote:

> Chinh Su Tran To wrote:
>
>> 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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>>
>>
> if flex residues used a value of 70e6 is seen this is a
> consequence/property of the molecule (discussed here).  Some years ago I
> worked with tr.  The substrate bindg site is a hphobic wall that doesn't
> lend itself to docking, is your bind site away from here?   Do a rigid run
> at telo bind site.
>
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