ADL: Error in binding energy calculations

Gavin Seddon home at gavsed.net
Thu Apr 2 06:21:56 PDT 2009


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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