ADL: Urgent for my Ph.D. thesis and my career

arijit basu arijit4uin at
Sun Apr 12 05:09:05 PDT 2009

No software is bad we all should be grateful to scripps research for providing the software free. Docking softwares are the tools/guidelines some softwares, search algo/ scoring func may good for one target no so good for other this does not make the software bad.

--- On Fri, 10/4/09, mswingle at <mswingle at> wrote:

From: mswingle at <mswingle at>
Subject: Re: ADL: Urgent for my Ph.D. thesis and my career
To: autodock at
Date: Friday, 10 April, 2009, 6:14 AM


It would be helpful if you could post more information from the dlg file. For example, what are the values of the different free energy components (electrostatic, internal energy etc.)? Do the structures of the docked complexes of these conformers look reasonable? 



----- Original Message -----
From: Mostafa El-Miligy <melmiligy4m at>
Date: Thursday, April 9, 2009 3:09 pm
Subject: ADL: Urgent for my Ph.D. thesis and my career
To: autodock at

> 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 because my Ph.D. supervisor Dr 
> Aly Hazzaa said that Autodock-4 is a bad software and not working 
> good. so please reply to me on this problem because it will affect my 
> career badly.
> Thank you
> Yours, 
> Mostafa El-Miligy
> Mostafa El-Miligy
> Ph.D. student 
> Department of Pharmaceutical Chemistry
> Faculty of Pharmacy
> University of Alexandria
> Egypt
> ________________________________________________
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