[BiO BB] plz help-DOCK 6.1

[Gary Van Domselaar]

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
> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>

-- 
Gary Van Domselaar, PhD
Associate Director, Bioinformatics.Org
gary at bioinformatics.org