ADL: Theory

Ruth Huey rhuey at scripps.edu
Sun Feb 16 08:28:30 PST 2014


A summary of the equations used in the AutoDock force field can be found here:
http://autodock.scripps.edu/resources/science/equations

More information is available:
http://autodock.scripps.edu/faqs-help/manual/autodock-4-2-user-guide
________________________________________
From: autodock-bounces at scripps.edu [autodock-bounces at scripps.edu] On Behalf Of Javeed ahmad [javeedahmadwar at yahoo.com]
Sent: Saturday, February 15, 2014 8:28 AM
To: autodock at scripps.edu
Subject: ADL: Theory

Hello friends,

Can someone please tell me what is the theory behind the calculation of the delta G values which Autodock predicts after docking.

 Regards
Javeed Ahmad War
DST INSPIRE Fellow
Ph.D. Research Scholar,
Department of Chemistry,
Dr. Harisingh Gour University,
Sagar, M.P., India-470003


________________________________
 From: "autodock-request at scripps.edu" <autodock-request at scripps.edu>
To: autodock at scripps.edu
Sent: Friday, February 14, 2014 12:00 PM
Subject: autodock Digest, Vol 114, Issue 8


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Today's Topics:

   1.  Blind docking or local docking (Hemendra Pal Singh Dhaked)
   2. Re:  Blind docking or local docking (vadiraj kurdekar)


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Message: 1
Date: Fri, 14 Feb 2014 09:18:43 +0530
From: Hemendra Pal Singh Dhaked <hemendrapsd at gmail.com>
Subject: ADL: Blind docking or local docking
To: autodock at scripps.edu
Message-ID:
    <CALHpLTTgeYkZHaj_Hf0q4L_sJd5AYQ7_+MZSzrjR4Waoi-cNAA at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Dear all
i am using AutoDock4.2. i have large size of protein for docking. To cover
entire surface of protein if i increase the of grid size upto 170 *170*170
with grid spacing of 0.375. such docking will be Blind docking or local
docking.
please tell me.

Thanks


------------------------------

Message: 2
Date: Fri, 14 Feb 2014 19:45:44 +0800 (SGT)
From: vadiraj kurdekar <vadirajgcppc at yahoo.co.in>
Subject: Re: ADL: Blind docking or local docking
To: "autodock at scripps.edu" <autodock at scripps.edu>
Message-ID:
    <1392378344.5393.YahooMailNeo at web192901.mail.sg3.yahoo.com>
Content-Type: text/plain; charset=iso-8859-1

Hi?Hemendra

you are performing?blind docking. you may end up with wrong results. identify binding pockets based on literatures or cocrystalized ligands or by using active site prediction softwares like
1. DoGSiteScorer: Active Site Prediction and Analysis Server http://dogsite.zbh.uni-hamburg.de/
2. http://bioinformatics.cm-uj.krakow.pl/activesite/
3. http://proline.physics.iisc.ernet.in/pocketdepth/

With Regards,
?
Vadiraj Kurdekar,
Research Scholar, Pharmacy Dept.,
Birla Institute of Technology and Science-Pilani,
Pilani Campus,?
Rajasthan, PIN: 333031
India.
Mobile: + 91 9460763664

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?



On Friday, 14 February 2014 9:39 AM, Hemendra Pal Singh Dhaked <hemendrapsd at gmail.com> wrote:

Dear all
i am using AutoDock4.2. i have large size of protein for docking. To cover
entire surface of protein if i increase the of grid size upto 170 *170*170
with grid spacing of 0.375. such docking will be Blind docking or local
docking.
please tell me.

Thanks
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