ADL: Theory

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ADL: Theory

Javeed ahmad
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: "[hidden email]" <[hidden email]>
To: [hidden email]
Sent: Friday, February 14, 2014 12:00 PM
Subject: autodock Digest, Vol 114, Issue 8
 

Send autodock mailing list submissions to
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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)


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

Message: 1
Date: Fri, 14 Feb 2014 09:18:43 +0530
From: Hemendra Pal Singh Dhaked <[hidden email]>
Subject: ADL: Blind docking or local docking
To: [hidden email]
Message-ID:
    <[hidden email]>
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 <[hidden email]>
Subject: Re: ADL: Blind docking or local docking
To: "[hidden email]" <[hidden email]>
Message-ID:
    <[hidden email]>
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 <[hidden email]> 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
****************************************
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Re: ADL: Theory

Ruth Huey
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: [hidden email] [[hidden email]] On Behalf Of Javeed ahmad [[hidden email]]
Sent: Saturday, February 15, 2014 8:28 AM
To: [hidden email]
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: "[hidden email]" <[hidden email]>
To: [hidden email]
Sent: Friday, February 14, 2014 12:00 PM
Subject: autodock Digest, Vol 114, Issue 8


Send autodock mailing list submissions to
    [hidden email]

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
    [hidden email]

You can reach the person managing the list at
    [hidden email]

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 <[hidden email]>
Subject: ADL: Blind docking or local docking
To: [hidden email]
Message-ID:
    <[hidden email]>
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 <[hidden email]>
Subject: Re: ADL: Blind docking or local docking
To: "[hidden email]" <[hidden email]>
Message-ID:
    <[hidden email]>
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 <[hidden email]> 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
****************************************
________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---

________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---