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

Trent E. Balius tbalius at aol.com
Tue Dec 16 08:44:40 PST 2014


 Hi Miranda,

I wrote a python script to look for broken molecules in the topdock file.  

This script is now available here:

  http://docking.org/~tbalius/Code.html

I hope this helps,

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: Trent E. Balius <tbalius at aol.com>
Cc: dock-fans <dock-fans at docking.org>
Sent: Tue, Dec 16, 2014 7:56 am
Subject: Re: DOCK3.6 output broken compounds, hydrogen and sulfur swap


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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