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

Trent E. Balius tbalius at aol.com
Fri Dec 12 15:08:06 PST 2014

 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 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?



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

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