ADL: autodock Digest, Vol 44, Issue 10

Eshita Sharma eshu10 at gmail.com
Fri Nov 9 05:20:32 PST 2007


I have been tring to dock ligands from a ligand database to a protein
and wanted to know if there were some genweric negative controls that
are used while doing docking studies with autodock 3 or autodock4.

Thank you
Eshita Sharma
Int PhD
Indian Institute of Science
Bangalore -560012
India

On Nov 9, 2007 1:30 AM,  <autodock-request at scripps.edu> wrote:
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> Today's Topics:
>
>    1.  Docking a ligand with known general positioning. (Mona N. Rahman)
>    2. Re:  need help for virtualscreening (Changming Lee)
>    3. Re:  need help for virtualscreening (Changming Lee)
>    4. Re:  need help for virtualscreening (Wilfred Li)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 8 Nov 2007 13:41:21 -0500 (EST)
> From: "Mona N. Rahman" <rahmanm at post.queensu.ca>
> Subject: ADL: Docking a ligand with known general positioning.
> To: autodock at scripps.edu
> Message-ID: <1353.130.15.147.135.1194547281.squirrel at post.queensu.ca>
> Content-Type: text/plain;charset=iso-8859-1
>
> To whom it may concern
>
> I am trying to dock a variety of potential inhibitory compounds into the
> active site of my enzyme.  They are quite similar so the purpose is to
> quantitate binding efficiency in the models by getting values for binding
> energy.  Seeing as I have an idea as to how they will bind in the active
> site, is there a way to tell the program how to position the ligand i.e.
> specific group on one side.
>
> Thank you
> Mona Rahman
>
>
>
> --
> Mona N. Rahman, Ph.D.
> Post-doctoral Fellow
> Botterell Hall, Room 634
> Department of Biochemistry
> Queen's University
> Kingston, ON, K7L 3N6
> Tel:  613-533-6392
> E-mail:  rahmanm at post.queensu.ca
>
>
>
> ------------------------------
>
> Message: 2
> Date: Fri, 9 Nov 2007 02:44:09 +0800
> From: Changming Lee <bright-_-lee at hotmail.com>
> Subject: Re: ADL: need help for virtualscreening
> To: <autodock at scripps.edu>
> Message-ID: <BAY125-W23D0ECB880066DA373B6D0FE8B0 at phx.gbl>
> Content-Type: text/plain; charset="gb2312"
>
> Its OK now, thank you.
>
> Mark
>
>
>
> > Date: Thu, 8 Nov 2007 10:34:27 -0800> From: sargis at scripps.edu> To: autodock at scripps.edu> Subject: Re: ADL: need help for virtualscreening> > Changming Lee wrote:> > hi all,> > > > could anyone tell me why the system tell me"/export/cvs: no such repository" after I type these command:> > > > setenv CVSROOT :pserver:anonymous at moses.scripps.edu:/export/cvsecho $CVSROOTcvs login> > http://mgldev.scripps.edu/pipermail/autodock/2007-October/002922.html> > The host and the path for the CVS has been changed. Please use:> > setenv CVSROOT :pserver:anonymous at mgl1.scripps.edu:/opt/cvs> > http://mgltools.scripps.edu/documentation/how-to/anonymous-access-to-our-cvs-repository> > -Sargis> ________________________________________________> --- ADL: AutoDock List --- http://autodock.scripps.edu/mailing_list ---
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> ------------------------------
>
> Message: 3
> Date: Fri, 9 Nov 2007 02:45:05 +0800
> From: Changming Lee <bright-_-lee at hotmail.com>
> Subject: Re: ADL: need help for virtualscreening
> To: <autodock at scripps.edu>
> Message-ID: <BAY125-W2684EBB3D83407DC7789F7FE8B0 at phx.gbl>
> Content-Type: text/plain; charset="gb2312"
>
> Its OK now, thank you.
>
> Mark
>
> > Date: Thu, 8 Nov 2007 10:34:27 -0800> From: sargis at scripps.edu> To: autodock at scripps.edu> Subject: Re: ADL: need help for virtualscreening> > Changming Lee wrote:> > hi all,> > > > could anyone tell me why the system tell me"/export/cvs: no such repository" after I type these command:> > > > setenv CVSROOT :pserver:anonymous at moses.scripps.edu:/export/cvsecho $CVSROOTcvs login> > http://mgldev.scripps.edu/pipermail/autodock/2007-October/002922.html> > The host and the path for the CVS has been changed. Please use:> > setenv CVSROOT :pserver:anonymous at mgl1.scripps.edu:/opt/cvs> > http://mgltools.scripps.edu/documentation/how-to/anonymous-access-to-our-cvs-repository> > -Sargis> ________________________________________________> --- ADL: AutoDock List --- http://autodock.scripps.edu/mailing_list ---
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> ------------------------------
>
> Message: 4
> Date: Thu, 8 Nov 2007 11:07:04 -0800
> From: "Wilfred Li" <wilfred at sdsc.edu>
> Subject: Re: ADL: need help for virtualscreening
> To: <autodock at scripps.edu>
> Message-ID: <452F37AE49199D49B1702D7D45038C4DC9302C at et.ad.sdsc.edu>
> Content-Type: text/plain;       charset="us-ascii"
>
> CVS Access
> export CVSROOT=:pserver:anonymous at mgl1.scripps.edu:/opt/cvs
>
> http://mgltools.scripps.edu/documentation/how-to/anonymous-access-to-our
> -cvs-repository
>
> Regards,
>
> Wilfred
>
>         -----Original Message-----
>         From: autodock-bounces at scripps.edu
> [mailto:autodock-bounces at scripps.edu]
>         On Behalf Of Changming Lee
>         Sent: Thursday, November 08, 2007 10:18 AM
>         To: autodock at scripps.edu
>         Subject: ADL: need help for virtualscreening
>
>         hi all,
>
>         could anyone tell me why the system tell me"/export/cvs: no such
>         repository" after I type these command:
>
>         setenv CVSROOT
> :pserver:anonymous at moses.scripps.edu:/export/cvsecho
>         $CVSROOTcvs login
>
>         thanks,
>
>         Mark
>
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> End of autodock Digest, Vol 44, Issue 10
> ****************************************
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