ADL: autodock Digest, Vol 67, Issue 2

jose correa corrjose at gmail.com
Sat Mar 6 12:30:52 PST 2010


As we see sometimes proteins are crystallized with few? molecules of water.
but? when we do protein preparation for docking we remove those water
molecules.
So is there any method? by which i can include these crystallized water
molecules in my docking studies using auto dock. how can i define these
water molecules while docking or preparing input files?

Dear
First, you need to be sure that your protein have structural water, if it is
ok, get a 3-D structure from PDB one of these and identify what are the
water molecules, then, when you clean the protein by the docking, try to
mantain those waters that are of your interes, you can do it by using a text
editer.
Best wishes
José Correa-Basurto

2010/3/6 <autodock-request at scripps.edu>

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> Today's Topics:
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>   1. Re:  Autodock 3.05 under ADT 1.5.4 (Stefano Forli)
>   2.   How to include crystallized waters in docking studies
>      (c c)
>   3. Re:  How to include crystallized waters in docking studies
>      (vivek kumar)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 5 Mar 2010 15:33:54 -0800
> From: Stefano Forli <forli at scripps.edu>
> Subject: Re: ADL: Autodock 3.05 under ADT 1.5.4
> To: "autodock at scripps.edu" <autodock at scripps.edu>
> Message-ID: <4B9194E2.90804 at scripps.edu>
> Content-Type: text/plain; charset="ISO-8859-1"; format=flowed
>
> Hi Tom,
>
> the flexible residues in AutoDock 4.x are an option, sorry for not making
> this clear
> enough in the tutorial.
> The most suitable option for you is the second one you mention: simply
> ignore any
> operation related to flexible residues.
>
> In the tutorial "Using AutoDock 4 with ADT" available here:
>
> http://autodock.scripps.edu/faqs-help/tutorial/using-autodock-4-with-autodocktools
> just skip the Exercise 7.
>
> Hope this helps,
>
> Stefano
>
>
> Tom Scior wrote:
> > Hello Autodock users,
> > here is a question, if one wishes to use
> > Autodock 4.2 under AutoDockTools 1.5.4,
> > but not with flexible amino acid sidechains
> > of recpetors, yet using the scoring
> > functions and GALS etc. of the newest release,
> > which options may one have?
> > 1) Switch to the AUTODOCK 3.05 option upon
> > launching ADT ?  Does this keep the new
> > scoring funtions of the AD4.2 release etc.
> > or does it work with the scoring - parameters of
> > the  old release AD3.05 ?
> > 2) Switch to the AUTODOCK 4.2 option upon
> > launchng ADT and skipping the FLEXIBLE RESIDUES
> > preprations (HOW? the Tutorial does not say) or
> > 3) Prepare one GLYCINE as the flexible amino acid
> > under AD4.2 (and follow the Tutorial UsingAutoDock4with) ?
> > Sorry for disturbing, but I could not find answer in
> > the documentation and Web.
> > Thank you, I appreciate your reply in advance
> > tom
> > ________________________________________________
> > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>
>
> --
>  Stefano Forli, PhD
>
>  Research Associate
>  Olson Molecular Graphics Laboratory
>  Dept. Molecular Biology,  MB-5
>  The Scripps Research Institute
>  10550  North Torrey Pines Road
>  La Jolla,  CA 92037-1000,  USA.
>
>     tel: (858) 784-2055
>     fax: (858) 784-2860
>     email: forli at scripps.edu
>     http://www.scripps.edu/~forli/
>
>
> ------------------------------
>
> Message: 2
> Date: Sat, 6 Mar 2010 18:58:00 +0530
> From: ankita kumari <akku8j at gmail.com>
> Subject: ADL:  How to include crystallized waters in docking studies
> To: autodock at scripps.edu
> Message-ID:
>        <7f5497b71003060528q5dd3136fqd8d07ea4c9da46e5 at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> To all users
>
> As we see sometimes proteins are crystallized with few  molecules of water.
> but  when we do protein preparation for docking we remove those water
> molecules.
>
> So is there any method  by which i can include these crystallized water
> molecules in my docking studies using auto dock. how can i define these
> water molecules while docking or preparing input files?
>
>
>
>
>
>
>
>
> --
> WITH REGARDS
>
> c
>
> ------------------------------
>
> Message: 3
> Date: Sat, 6 Mar 2010 21:22:29 +0530 (IST)
> From: vivek kumar <mbi_vivekg at yahoo.co.in>
> Subject: Re: ADL: How to include crystallized waters in docking
>        studies
> To: autodock at scripps.edu
> Message-ID: <939171.80361.qm at web94007.mail.in2.yahoo.com>
> Content-Type: text/plain; charset=iso-8859-1
>
>
> hello ankita , you are going right.I donot know? any method.you can talk to
> any other experts.because i have left? bioinformatics line after m.sc. ok
> --- On Sat, 6/3/10, ankita kumari <akku8j at gmail.com> wrote:
>
> From: ankita kumari <akku8j at gmail.com>
> Subject: ADL:  How to include crystallized waters in docking studies
> To: autodock at scripps.edu
> Date: Saturday, 6 March, 2010, 6:58 PM
>
> To all users
>
> As we see sometimes proteins are crystallized with few? molecules of water.
> but? when we do protein preparation for docking we remove those water
> molecules.
>
> So is there any method? by which i can include these crystallized water
> molecules in my docking studies using auto dock. how can i define these
> water molecules while docking or preparing input files?
>
>
>
>
>
>
>
>
> --
> WITH REGARDS
>
> ANKITA
> ________________________________________________
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> End of autodock Digest, Vol 67, Issue 2
> ***************************************
>



-- 
Ph.D. JOSE CORREA BASURTO Professor of Pharmacology, Department of
Biochemistry and Pharmacology, Escuela Superior de Medicina, Instituto
Politécnico Nacional, México. Plan de San Luis Y diaz Mirón S/N, Col. Casco
de Santo Tomas, Mexico city, México. CP: 11340. Tel/Fax; (+5255) 57296000
Ext 62747 and 62767 e:mail: josecorreabasurto at hotmail.com or jcorreab at ipn.mx,
corrjose at gmail.com
website: http://farmacologiacomputacional.blogspot.com/


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