[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:

 http://link.springer.com/article/10.1007/s10822-012-9565-y

Here is the link to download SB2012.  

http://ringo.ams.sunysb.edu/index.php/SB2012

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

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: 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?
http://ringo.ams.sunysb.edu/index.php/2015_DOCK_tutorial_with_Poly(ADP-ribose)_polymerase_(PARP)#Large-vs.in



Thanks,
Jonathan



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

Hi,

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

scott









-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mailman.docking.org/pipermail/dock-fans/attachments/20160325/109e27b5/attachment.html 


More information about the Dock-fans mailing list