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 Post subject: Blind docking
PostPosted: Mon Nov 23, 2009 5:10 am 
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Millimolar User
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Joined: Mon Nov 23, 2009 4:26 am
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Dear Autodock users;

I am new to autodock and want to use it for blind docking.I donot know my docking site and set the box size to 80**3 (which I think is taken to be 64**3 as default, please correct me if I am wrong), but it gives error regarding energy being infinite. In forum some replies indicate that by keeping box set to 63**3 or 64**3 can resolve the issue.

but by keeping 64**3 as box size donot cover my system and I donot know where docking can occur. Should I do docking in steps by using 64**3 box but centred at different atoms.

Any suggestion is highly appreciated.

Thanks and regards;
VM


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 Post subject: Re: Blind docking
PostPosted: Wed Jan 27, 2010 1:17 am 
It will be necessary to set up the dockings to search the entire surface of the protein (or other macromolecule) of interest. This can be achieved using AutoGrid to create very large grid maps, with the maximum number of points in each dimension, and if necessary, creating sets of adjacent grid map volumes that cover the macromolecule. The third-party tool BDT can be used to set up such sets of grid maps.


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 Post subject: Re: Blind docking
PostPosted: Fri Jan 29, 2010 11:24 pm 
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The 64 grid point limitation is only in the Cygwin version. The regular Linux/Unix version is 128. If 64x64x64 at your current grid spacing is too small, you can increase the spacing to make the grid larger (you should probably keep spacing under 1 Angstron).

Personally, I think you'd be better off using some kind of active site detection software (e.g. http://sts.bioengr.uic.edu/castp/index.php ) to identify candidate binding pockets and set up separate docking runs for each one.


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 Post subject: Re: Blind docking
PostPosted: Sat Apr 07, 2012 2:04 pm 
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I wonder if there is a script, which defines automatically the optimal coordinates of center location for the blind docking in such a way to cover all the protein, but minimize size of the grid? Anyway, are there any scripts which can define center of coordinates automatically from PDB file without Autodock tools usage or maybe it is possible to use Autodock tools in command line mode for this purpose?


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