[Dock-fans] ligand -regding

John J. Irwin jji at cgl.ucsf.edu
Thu Dec 6 12:02:09 PST 2007

Hi Vinay

Since you are using ISIS Draw -> (Open?) Babel, Babel should look after
adding all protons. You need to pay attention to the protonation,
charge, and tautomeric form (if relevant) of your molecule created in
this way.

All versions of DOCK support several scoring functions, and rather than
repeat what is in the manual, I'll just refer you here to the manual and
the literature for guidance about which one is most appropriate for your

Hope this helps


Vinay Kumar wrote:
> Hi again,
> I use MDL ISIS draw (free) software for drawing my ligands, save it,
> and port it through Babel, which would give me, mol2 or pdb output
> files, which i can use as input ligand file in DOCK. i hope this is
> what was asked for!! (and please tell me, if my method mentioned above
> is ok?)
> is there anyway, i can know, what scoring function is in use, and can
> i change it in DOCK?
> With regards,
> Vinay
> On Dec 2, 2007 11:16 AM, John J. Irwin <jji at cgl.ucsf.edu> wrote:
>> Hi Vinay
>> It would be helpful for you to tell us a bit more about what program(s)
>> and options you are using. Which version of docking software? Which
>> drawing interface?
>> In general, if you are using a united-atom scoring function, then you
>> only want polar hydrogens on the protein. If you are using an all atom
>> scoring function, then you will need all H atoms to be explicit. You
>> always need (at least for all versions of DOCK) a ligand with all atoms
>> explicitly represented, for example as found in ZINC.
>> Good luck
>> John
>> johnirwin.docking.org
>> Vinay Kumar wrote:
>>> Hello dockers,
>>> I would like to know,
>>> 1) why is it that only polar hydrogens are added in the macromolecule?
>>> 2) if we need to add all hydrogens (polar and non-polar) explicitly to
>>> the ligand while a docking is performed? for ex- if the ligand is
>>> phenol, do i have to draw the phenyl ring with CH2 explicitly shown,
>>> or just use the ring structure provided by the drawing interface?
>>> would like your thoughts,
>>> regards,
>>> Vinay
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