[Dock-fans] DOCK3.6 output broken compounds, hydrogen and sulfur swap

Yi Shang mirandaisbest at gmail.com
Tue Dec 16 07:56:02 PST 2014


Hi Trent,
How do you filter out the broken molecules? Thanks!


On Fri, Dec 12, 2014 at 6:08 PM, Trent E. Balius <tbalius at aol.com> wrote:
>
>  Hi Miranda,
>
> Yes, DOCK 3.6 does produece broken molecules .
> The best thing is to filter out the broken molecules.
>
> These problems are fixed in DOCK 3.7.
>
> Thanks for letting us know.
>
> Trent
>
>  ======================================
> Trent E. Balius, PhD
> Postdoc, Shoichet Lab,
> Dept. Pharm. Chem., UCSF
> Phone: (415) 514-4253
> URL: http://docking.org/~tbalius
> ======================================
>
>
>  -----Original Message-----
> From: Yi Shang <mirandaisbest at gmail.com>
> To: dock-fans <dock-fans at docking.org>; Trent Balius <tbalius at aol.com>
> Sent: Fri, Dec 12, 2014 2:55 pm
> Subject: DOCK3.6 output broken compounds, hydrogen and sulfur swap
>
>  Hi All,
> I am having some weird broken compounds in my topdock.py pdb output. And
> they seem to contain specific functional groups like O=S=O.
>
>  For example
> https://dl.dropboxusercontent.com/u/76890735/trouble.pdb  is one of the
> pdb output that seems to have one sulfur and one hydrogen swapped in 3D
> coordinates.
>
>  https://dl.dropboxusercontent.com/u/76890735/21_0.265.db.gz  is the
> flexible database downloaded from ZINC, which contains the that compound
> above.
>
>  https://dl.dropboxusercontent.com/u/76890735/zinc_2804795.ddb is db
> format file for the same compound that I downloaded directly from ZINC. It
> matches 21_0.265.db.gz, so I think the pdb problem happens after DOCK3.6
> reads in 21_0.265.pdb.gz.
>
>  Does anyone have any experience with this?
>
>  Thanks!
>
>  --
>  Yi  Shang,   Ph.D.
> postdoctoral research associate
> Icahn School of Medicine at Mount Sinai
>
>
>

-- 
Yi  Shang,   Ph.D.
postdoctoral research associate
Icahn School of Medicine at Mount Sinai
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