[Dock-fans] dock6.6

Trent E. Balius tbalius at aol.com
Mon Jul 15 10:01:38 PDT 2013


Hi Mahesh,

Identify a side chain of your protein that forms part of the pocket
and is located in the center of the pocket.
Delete all of the protein, but this side chain and save as a mol2 file. 

Give this file to sphereselector instead of the ligand mol2 file.

Does this make since?

This is one solution.  There are many other possible work arounds.

I hope this helps,

Trent

======================================
Trent E. Balius, PhD
Shoichet Lab – Faculty of Pharmacy,
University of Toronto
Office Phone: (416) 946-7304
Cell Phone: (516) 381-0926
URL: http://docking.org/~tbalius
======================================


---- Original Message ----
From: Mahesh Hegde <mahesh at biochem.iisc.ernet.in>
To: Trent E. Balius <tbalius at aol.com>
Sent: Mon, Jul 15, 2013 12:10 pm
Subject: Re: [Dock-fans] dock6.6


Hi, thank for your mail, i have checked those tutorials. SPHGEN will
generate different possibilities of ligand binding site on protein 
right?
and then on what basis it will select perticular sphere? and is it
possible to change it manually? because in my case i can see nice cavity
inside the protein but my ligand is not fitting inside that, rather its
attached to outer surface somewhere else, i checked the sphere selected,
which is the outer surface, so how perfect sphere will get selected?
> Hi Mahesh,
>
> Here is a good tutorial on running DOCK6.6:
>
> 
http://ringo.ams.sunysb.edu/index.php/2013_DOCK_tutorial_with_Orotodine_Monophosphate_Decarboxylase
> http://ringo.ams.sunysb.edu/index.php/DOCK_Tutorials
>
> Q1:
> Note that Sphere selector uses a mol2 file of a ligand usually to
> select the spheres.  The ligand usually defines a binding site on your
> protien.  If you are using multiple structures of the same protein it
> might be advisable to align them it to the same frame.  this can be
> done with Chimera for example.
>
> Q2:
> There are two separate task in docking:
> (1) sampling:
> http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#LigandFlexibility
> (2) scoring:
> http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#Scoring
> the choice of sampling method and scoring method will effect your
> results.
> You should use Anchor and grow method (sampling) and Grid score
> (scoring).
> I would suggest using the Tutorial above to guide you.
> I would also suggest using the manual as a reference:
> http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm
>
> I hope this helps,
>
> Trent
>
>
> ======================================
> Trent E. Balius, PhD
> Shoichet Lab – Faculty of Pharmacy,
> University of Toronto
> Office Phone: (416) 946-7304
> Cell Phone: (516) 381-0926
> URL: http://docking.org/~tbalius
> ======================================
>
>
> ---- Original Message ----
> From: Mahesh Hegde <mahesh at biochem.iisc.ernet.in>
> To: dock-fans <dock-fans at docking.org>
> Sent: Mon, Jul 15, 2013 10:09 am
> Subject: [Dock-fans] dock6.6
>
>
>
>
>
> Hi, My name is Mahesh, i have started using  Dock6.6 recently. I have
> got
> few problems and doubts as well, it might be basic for you people, 
so..
> Some dms file (from same protein but different pdb files) are not able
> to
> make any clusters when  i select sphere selectors, but some can form,
> what
> could be the reason?
>
> I have one basic question, in dock6.6 there are 4 different types, 
amber
> scoring and docking, anchor and grow docking, mpi docking, solvation
> energy docking, so , on what preference i should select these 
programs?
> and are these going to give different result?
>
> Thank you very much for your time.
>
>
>
> --
> Sincerely,
> Mahesh Hegde
>
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--
Sincerely,
Mahesh Hegde

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