[Zinc-fans] requesting peer suggestions on docking and duplication

[Zsolt Zsoldos]

John,

I know it is not exactly the profile of ZINC/DUD to work with PDB complexes,
but would you be interested to setting up a correctly protonated complex
database for cognate docking benchmarks ?

Egon Willighagen has asked this on my blog in response to my detailed
version of the protonation post:
http://www.simbiosys.ca/blog/2008/05/17/correct-protonation-state-for-docking/#comment-1377

"Is there a gold standard; a good training set to set approaches on? As you
already said, crystallography is not going to help. Databases with
experimental pKa database are often proprietary… Any suggestions?"

Since I do not know any public database with validated correct protonation
assignement for specific complexes, it would be a very valuable thing to
create. I am thinking about a community based peer-reviewed project, kind of
like Wikipedia, where people could edit/comment/curate the data. I would be
interested to help, deposit PDB complexes processed by our software. But I
think it would be better if it is not hosted by us (commercial software
vendor), I would not want it to be biased, so docking.org would be the
perfect entity to house it.

Zsolt (aka ZZ)

On Sat, May 17, 2008 at 10:18 AM, John J. Irwin <jji at cgl.ucsf.edu> wrote:

> Hi Elite
> >>>
> >>> The question is, if we merge all the files into one single giga SDF
> >>> file, are the ZINC IDs unique to all the entries, meaning, can we
> >>> safely traceback the ligand of interest to its representative pH
> >>> subset?
> >>>
> You may not be able to, since we use the same ZINC ID for all
> representations that can interconvert freely in buffer. If it is
> important to you to know, I suggest just merging _within_ each pH subset.
>
> John
> UCSF ZINC Team
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