[Dock-fans] RE: [Dockdev] Docking and Scoring algorithms

Szilveszter Juhos szilva.juhos at gmail.com
Thu Feb 24 11:33:47 PST 2005

Hello All, 

I do not want to repeat issues written in the previous mails, simply
want to emphasize that there is a real need for fast and accurate
binding energy estimation. Fast means hours instead of weeks, accurate
means being good enough to rank hits. When there is a huge virtual
library with millions of compounds and finally one gets 30K hits, it
is not so obvious to filter out the bad ones.

Using FEP one have the trivial problem of loosing diversity. If I want
unseen chemical entities how to get their dG without measuring it in
the wet lab? Not speaking about the fact that many of the dG values
form experiments are rubbish, simply can not be used for docking
validation (or for anything at all) (sorry).

To cut it short, what I want to say is that chemists always will
complain that docking is not providing correct binding energies. It is
a convenient excuse to say "docking is not for dG estimation" but they
are complaing righfully since they badly need a (fast, accurate)
method to do it. Probably it will be something but docking or FEP but
since that "if all you have is a hammer everything looks like a nail".


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