[BiO BB] plz help-DOCK 6.1

[Mike Marchywka]

Is there a list of these things somewhere- like a wiki page? Specifically
limitations versus needs for prediction,modelling,  and visualization?
I've got my
opengl/c++ molecule viewer almost working ( the UI and scripting ability 
took
more effort than the "real" stuff) and now I need something useful to do 
with it.
Right now I'm not sure it has any benefit over RasMol-
I can draw some nice pictures with "artisitic" potential surfaces but maybe 
I can
find something scientifically interesting. In as much as cavity 
visualization was an early
objective, maybe I can find a way to do some active site or interaction  
predictions.

I had asked earlier about more realistic potential surfaces and assumed the 
lack of
response indicated lack of interest in the area.

Obviously visuals don't do predictions
but they can be good tools for testing/evaluating these things.

Thanks.




>From: Gary Van Domselaar <gary at primary.bioinformatics.org>
>Reply-To: "General Forum at Bioinformatics.Org" 
><bio_bulletin_board at bioinformatics.org>
>To: ritu chaudhary <ritu.bioinfo at gmail.com>
>CC: bio_bulletin_board at bioinformatics.org
>Subject: Re: [BiO BB] plz help-DOCK 6.1
>Date: Mon, 2 Apr 2007 10:24:08 -0400 (EDT)
>
>
>Hi ritu,
>
>
>Wow, you sure sound desperate.
>
>You should check out the ZINC database (designed to work with dock), it 
>will give you the prepped small molecules for running with DOCK.
>http://blaster.docking.org/zinc/
>
>And may have better subsets than NCI (you do mean NCI don't you?)  for 
>screening against NS3 protease.
>
>Zinc and Dock also having their own mailing lists that might serve you 
>better in answering  this question.
>http://blur.compbio.ucsf.edu/mailman/listinfo
>
>Kindest Regards,
>
>g.
>--
>Gary Van Domselaar, PhD
>Associate Director, Bioinformatics.Org
>gary at bioinformatics.org
>
>
>On Mon, 2 Apr 2007, ritu chaudhary wrote:
>
>><arnold at cabm.rutgers.edu>
>>>
>>>    I am working on project entitled *"Virtual Screening of Inhibitors
>>>against NS3 Protease of Dengue Virus"* using software *Dock 6.1*.Sir i
>>>have to perform Docking of 1bef.pdb to about 1000 compounds of NCL
>>>library. i read all the tutorials given at site
>>>http://dock.compbio.ucsf.edu/DOCK_6/index.htm
>>>and i used them for running dock 6 but those tutorials are for docking
>>>single ligand to the receptor.and i want to dock a database containing
>>>10,000 compounds.so plzzzzzzzzzzzzzz tell me that tutorial which is for
>>>docking a library of compounds to single 3-D receptor mol.
>>>please help me.
>>>i have prepared receptor mol by running SPHGEN and it has generated 27
>>>clusters and now i have to generate spheres on the surface of receptor so
>>>which tutorial should i follow for that
>>>I will be really thankful.
>>>
>>>Ritu Chaudhary
>>>M.Sc BIOINFORMATICS
>>>CCSHAU
>>>HISAR
>>>INDIA
>>>
>>>
>>>
>>>
>>>
>>>
>>_______________________________________________
>>General Forum at Bioinformatics.Org - 
>>BiO_Bulletin_Board at bioinformatics.org
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>>
>
>--
>Gary Van Domselaar, PhD
>Associate Director, Bioinformatics.Org
>gary at bioinformatics.org
>_______________________________________________
>General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org
>https://bioinformatics.org/mailman/listinfo/bio_bulletin_board

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