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

Jonathan Gough jonathan.d.gough at gmail.com
Wed Mar 23 09:34:22 PDT 2016


Thanks Dwight.

On Wed, Mar 23, 2016 at 12:27 PM, Dwight McGee <dwight.mcgee at gmail.com>
wrote:

> Hi Jonathan,
>
> As a general of rule of thumb, for dealing with explicit waters that are
> retained for docking purposes.  I make sure that the hydrogen atoms of the
> receptor and water molecule are oriented correctly such that the distance
> and angle meet the criteria that you set for a hydrogen bond. In addition,
> we have run a short minimization with heavy restraints on the heavy atoms
> in order to maximize the h-bond interactions. We visualized the minimized
> structure just to make sure that the h-bond network is still maintained.
>
> Once satisfied we used that structure as our receptor for the docking
> calculations.
>
> Hopefully, this helps when moving on to other systems once you are
> successful with the pygm test case.
>
> Best,
> Dwight
>
>
> On Wed, Mar 23, 2016 at 12:06 PM, Trent E. Balius <tbalius at aol.com> wrote:
>
>> Hi Jonathan,
>>
>> Question1.
>>   A subset of the systems of the DUDE systems are distributed with
>> SB2010/SB2012
>>   which are prepared for DOCK6
>>   Otherwise, you will need to prepare the receptors yourself,
>>   I would suggest using Chimera and its dock prep tool to help you
>> prepare the receptors.
>>   I would also suggest using the mol2 file distributed with DUDE
>> (audoDUDE is for DOCK3.7):
>>      http://dude.docking.org/
>>      here are the mol2 files:
>>      http://dude.docking.org/targets/aa2ar/actives_final.mol2.gz
>>      http://dude.docking.org/targets/aa2ar/decoys_final.mol2.gz
>> Question2:
>>   Including waters is possible in DOCK3.7 but a little tricky:
>>   see the following:
>>   http://wiki.bkslab.org/index.php/DOCK_3.7_tutorial_%28Anat%29
>>   you will need to use "blastermaster.py -v --addNOhydrogensflag"
>>
>>   For dock6 it is a little easier,  you just need to make sure that the
>> water
>>   is in the mol2 file (and it has the right partial charges and atom type
>> for grid to run properly).
>>
>> I hope that 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: Dwight McGee <dwight.mcgee at gmail.com>
>> Cc: dock-fans <dock-fans at docking.org>
>> Sent: Wed, Mar 23, 2016 7:28 am
>> Subject: Re: [Dock-fans] auto-DUD-e and explicit water -- Dock 6.7
>>
>> Hi Dwight,
>>
>> Not exactly. At the moment, I am simply trying to reproduce the docking
>> experiment for pygm. This is one of a few receptors in DUD-e that has an
>> explicit water present in the receptor.pdb.
>>
>> http://dude.docking.org/targets/pygm
>>
>> In general, we are looking at explicit waters and water structure and
>> would like to be able to use dock to run experiments with an explicit water
>> (hence trying to reproduce pygm to make sure we know what we are doing).
>>
>> Any insight would be appreciated,
>> Jonathan
>>
>> On Wed, Mar 23, 2016 at 10:16 AM, Dwight McGee <dwight.mcgee at gmail.com>
>> wrote:
>>
>>> Hi Jonathan,
>>>
>>>
>>> Pertaining to question #2. Are you trying to identify ligands that make
>>> a specific water mediated interaction with the receptor?
>>>
>>> Best,
>>> Dwight
>>>
>>> On Tue, Mar 22, 2016 at 7:17 PM, Jonathan Gough <
>>> jonathan.d.gough at gmail.com> wrote:
>>>
>>>> Hi all,
>>>>
>>>> 2 questions -
>>>>
>>>> 1. I was wondering if it is possible to use the files for auto-DUD-E in
>>>> testing for Dock 6.7. It seems as if everything is set up for 3.7, but not
>>>> for 6.7.
>>>>
>>>> Related to that, I tried using basic steps in the tutorials to
>>>> reproduce the binding of the x-ray crystal ligand from pygm (in the DUD-E)
>>>> using the ligand.mol2 and the receptor.pdb from
>>>> http://dude.docking.org/
>>>>
>>>> unfortunately, the generated poses were very far from expected.
>>>>
>>>> 2. when prepping the grid scoring function (or the pdb/mol2), is there
>>>> something special that I need to do to ensure that the explicit water is
>>>> treated correctly or to make sure that the water parameters are included?
>>>>
>>>> Thanks,
>>>> Jonathan
>>>>
>>>> _______________________________________________
>>>> Dock-fans mailing list
>>>> Dock-fans at docking.org
>>>> http://mailman.docking.org/mailman/listinfo/dock-fans
>>>>
>>>>
>>>
>>>
>>> --
>>> T. Dwight McGee Jr.
>>>
>>> dwight.mcgee at gmail.com
>>>
>>> "Problems cannot be solved at the same level of awareness that created
>>> them."
>>>                 Albert Einstein
>>>
>>
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>>
>
>
>
> --
> T. Dwight McGee Jr.
>
> dwight.mcgee at gmail.com
>
> "Problems cannot be solved at the same level of awareness that created
> them."
>                 Albert Einstein
>
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