ADL: autodock Digest, Vol 56, Issue 21

jose correa corrjose at gmail.com
Sun Apr 12 19:12:03 PDT 2009


Dear Mostafa
No always, the docking methods reproduces the affinity values obtained
by experimental data, if you have checked your protein and ligands and not
mistakes are these, you can try againg following the tutorial step by step.
Remember that some times the proteins have co-enzymes and structural waters
that need be considered, you can see this studying carefully its natural
enviroment.
Best wishes
Jose Correa-Basurto

2009/4/12 <autodock-request at scripps.edu>

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> Today's Topics:
>
>   1. Re:  Urgent for my Ph.D. thesis and my career (arijit basu)
>   2. Re:  Urgent for my Ph.D. thesis and my career (Gavin Seddon)
>   3. Re:  A help needed to start.... (bagdevi.mishra at gmail.com)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 12 Apr 2009 17:39:05 +0530 (IST)
> From: arijit basu <arijit4uin at yahoo.co.in>
> Subject: Re: ADL: Urgent for my Ph.D. thesis and my career
> To: autodock at scripps.edu
> Message-ID: <802859.44600.qm at web7603.mail.in.yahoo.com>
> Content-Type: text/plain; charset=iso-8859-1
>
> 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 jaguar1.usouthal.edu <
> mswingle at jaguar1.usouthal.edu> wrote:
>
>
> From: mswingle at jaguar1.usouthal.edu <mswingle at jaguar1.usouthal.edu>
> Subject: Re: ADL: Urgent for my Ph.D. thesis and my career
> To: autodock at scripps.edu
> Date: Friday, 10 April, 2009, 6:14 AM
>
>
> Mostafa,
>
> 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?
>
> Regards,
>
> Mark
>
> ----- Original Message -----
> From: Mostafa El-Miligy <melmiligy4m at yahoo.com>
> Date: Thursday, April 9, 2009 3:09 pm
> Subject: ADL: Urgent for my Ph.D. thesis and my career
> To: autodock at scripps.edu
>
>
> > 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
> >
> >
> >
> >? ? ???
> > ________________________________________________
> > --- ADL: AutoDock List? --- http://autodock.scripps.edu/mailing_list ---
>
> ________________________________________________
> --- ADL: AutoDock List? --- http://autodock.scripps.edu/mailing_list ---
>
>
>
>      Cricket on your mind? Visit the ultimate cricket website. Enter
> http://beta.cricket.yahoo.com
>
> ------------------------------
>
> Message: 2
> Date: Sun, 12 Apr 2009 13:27:29 +0100
> From: Gavin Seddon <home at gavsed.net>
> Subject: Re: ADL: Urgent for my Ph.D. thesis and my career
> To: autodock at scripps.edu
> Message-ID: <49E1DE31.7020103 at gavsed.net>
> Content-Type: text/plain; charset=iso-8859-1; format=flowed
>
> arijit basu wrote:
> > 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 jaguar1.usouthal.edu <
> mswingle at jaguar1.usouthal.edu> wrote:
> >
> >
> > From: mswingle at jaguar1.usouthal.edu <mswingle at jaguar1.usouthal.edu>
> > Subject: Re: ADL: Urgent for my Ph.D. thesis and my career
> > To: autodock at scripps.edu
> > Date: Friday, 10 April, 2009, 6:14 AM
> >
> >
> > Mostafa,
> >
> > 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?
> >
> > Regards,
> >
> > Mark
> >
> > ----- Original Message -----
> > From: Mostafa El-Miligy <melmiligy4m at yahoo.com>
> > Date: Thursday, April 9, 2009 3:09 pm
> > Subject: ADL: Urgent for my Ph.D. thesis and my career
> > To: autodock at scripps.edu
> >
> >
> >
> >> 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
> >>
> >>
> >>
> >>
> >> ________________________________________________
> >> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list---
> >>
> >
> > ________________________________________________
> > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
> >
> >
> >
> >       Cricket on your mind? Visit the ultimate cricket website. Enter
> http://beta.cricket.yahoo.com
> > ________________________________________________
> > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
> >
> >
> YES INDEED, well said.
>
>
> ------------------------------
>
> Message: 3
> Date: Sun, 12 Apr 2009 23:08:50 +0530
> From: bagdevi.mishra at gmail.com
> Subject: Re: ADL: A help needed to start....
> To: autodock at scripps.edu
> Message-ID:
>        <c1a055830904121038t5297d28eh1293a50dfdcf189a at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Try to reproduce the result of docking using the tutorial associated
> with autodock. By the time you end up with the works involved in the
> tutorial, you will learn the protocol.
>
> good luck.
>
> Regards,
> Bagdevi Mishra.
>
>
>
>
> On Sat, Apr 11, 2009 at 2:27 PM, Mahmoud A. A. Ibrahim
> <m.ibrahim1982 at yahoo.com> wrote:
> > Hi Guys
> > I posted one email asking for help and I haven't got any help.
> > I am new user here, and I don't know what should I read to learn
> Autodock, I read the tutorial 4 and the ppt, what else should I do?
> > Thanks in Advance
> > M. Ibrahim
> >
> > #######
> > The previous email:
> > Dear Users
> > This is my first day in this mailling list and at the same time the first
> time for me to learn docking.
> > So, I appreciate any recommendation and advise to help me to start on
> this subject.
> > I
> > attended just a few classes on docking, as a resultmy background is so
> > week. So, where should I start? what books or chapters should I read?
> > I took forward to hearing from you.
> > Sincerely.
> > M. Ibrahim
> > #########
> >
> >
> >
> > ________________________________________________
> > --- ADL: AutoDock List ?--- http://autodock.scripps.edu/mailing_list ---
> >
>
>
>
> ------------------------------
>
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>
> End of autodock Digest, Vol 56, Issue 21
> ****************************************
>

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