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

Dwight McGee dwight.mcgee at gmail.com
Wed Mar 23 09:27:21 PDT 2016


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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