[Dock-fans] auto-DUD-e and explicit water -- Dock 6.7

Trent E. Balius tbalius at aol.com
Fri Mar 25 07:32:53 PDT 2016

Hi Jonathan,

We prepared the DUD systems and they are available in SB2012:

This is discussed in this paper:


Here is the link to download SB2012.  


You could use the overlap (~38 systems) to get started.  

I hope this helps,


Trent E. Balius, PhD
Postdoc, Shoichet Lab, 
Dept. Pharm. Chem., UCSF
Phone: (415) 514-4253
URL: http://docking.org/~tbalius



-----Original Message-----
From: Jonathan Gough <jonathan.d.gough at gmail.com>
To: Scott Brozell <sbrozell at rci.rutgers.edu>
Cc: Dwight McGee <dwight.mcgee at gmail.com>; dock-fans <dock-fans at docking.org>; Trent E. Balius <tbalius at aol.com>
Sent: Thu, Mar 24, 2016 10:14 am
Subject: Re: [Dock-fans] auto-DUD-e and explicit water -- Dock 6.7

Does anyone know which of the DUDE sets has inputs for dock6.7?
Or can anyone recommend a set of comparable inputs/settings for getting comparable results using dock6.7?

Explicitly I'm looking for recommendations on what one would use for the dock6.7 equivalent of INDOCK and any recommendations on what scoring function(s) I aught to use. 

or how would they compare to the tutorial on the Risso Lav Tutorials page?


On Thu, Mar 24, 2016 at 3:19 AM, Scott Brozell <sbrozell at rci.rutgers.edu> wrote:


As far as the test diffs, they all look unsurprising and likely insignificant.


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