ADL: autodock Digest, Vol 114, Issue 8

Hemendra Pal Singh Dhaked hemendrapsd at gmail.com
Sat Feb 15 04:39:42 PST 2014


Thanks for answer.

Can you tell me the condition (Grid size and Grid spacing) for Local
docking and Blind docking.

Thanks


On Sat, Feb 15, 2014 at 1:30 AM, <autodock-request at scripps.edu> wrote:

> Send autodock mailing list submissions to
>         autodock at scripps.edu
>
> To subscribe or unsubscribe via the World Wide Web, visit
>         http://mgldev.scripps.edu/mailman/listinfo/autodock
> or, via email, send a message with subject or body 'help' to
>         autodock-request at scripps.edu
>
> You can reach the person managing the list at
>         autodock-owner at scripps.edu
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of autodock digest..."
>
>
> Today's Topics:
>
>    1.  Blind docking or local docking (Hemendra Pal Singh Dhaked)
>    2. Re:  Blind docking or local docking (vadiraj kurdekar)
>
>
> ----------------------------------------------------------------------
>
> 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
>
> ________________________________
>
> This e-mail (and any attachments), is confidential and may be privileged.
> It may be read, copied and used only by intended recipients. Unauthorized
> access to this e-mail (or attachments) and disclosure or copying of its
> contents or any action taken in reliance on it is unlawful. Unintended
> recipients must notify the sender immediately by e-mail/phone & delete it
> from their system without making any copies or disclosing it to a third
> person.
>
> ________________________________
>
> ?
> ?
> ?
>
>
>
> 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
> ________________________________________________
> --- ADL: AutoDock List? --- http://autodock.scripps.edu/mailing_list---
>
> ------------------------------
>
> ________________________________________________
> --- ADL: AutoDock List  ---
> http://www.scripps.edu/pub/olson-web/doc/autodock/ ---
>
> End of autodock Digest, Vol 114, Issue 8
> ****************************************
>


More information about the autodock mailing list