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

[John J. Irwin]

Hi Zsolt

Thanks for your comments. We agree, and look forward seeing the results 
of a more sophisticated treatment of protonation/tautomerism. You 
absolutely should evaluate the internal energy due to the cost of 
deprotonation and/or tautomerism. Unfortunately, this is often a pretty 
subtle thing to calculate even at a modestly high level of theory. ZINC 
provides a way to get started and anticipate these effects *now*, 
however imperfectly.

Cheers

John
UCSF ZINC Team


Zsolt Zsoldos wrote:
> Dear Elite158 and John,
>
> It is an excellent step to offer multiple protonation versions of the 
> molecules to help docking/screening runs.
> My sincere thanks to the ZINC team for that!
>
> However, I would like to make a note, that the problem is much deeper, 
> and proper choice of protonation really depends on local environment 
> in a protain-ligand binding scneraio, which cannot be sufficiently 
> modeled by a global property, like the pH. I have written response on 
> my blog about it and plan to folow up with more details this weekend:
> http://www.simbiosys.ca/blog/
>
> Zsolt
>
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