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

Szilveszter Juhos szilva.juhos at gmail.com
Sat Feb 26 12:06:41 PST 2005

On Sat, 26 Feb 2005 20:26:39 +0100, Vincent LEROUX
<Vincent.Leroux at edam.uhp-nancy.fr> wrote:
> I agree that most scoring functions are not correlated enough to the binding energies. But for me this is not as bad as it seems.

Certainly. All I wanted to say is that in practice there should be
something between MD and docking. My experience was that simply there
is no time to check all the possible hits with MD. It is not only the
CPU time but the file preparation also. In case of few hundreds of
possible leads the chemists will say finally: "OK, but sort these
somehow then we can start to work with the most promising ones".
Sometimes you must give an order in a week when project deadlines and
milestones are looming.

Unfortunatelly I have no chance to try SILVER but you made me curious.
Anyway it would be silly to rely on docking only and I doubt anybody
is doing it so.

I am not so pessimistic about docking since I saw few times that it
can really find good, specific new binders. My the problem arises not
at the "hit identification" but the "lead selection" and "lead
optimisation" phase of drug development.

> And if computer simulations were faster and more reliable than experiments, wouldn't 
> many of them lose their job? I am not sure that is what they need  ;-)

Well, put it like this: "both experimental results and simulations are
rubbish" to keep everybody unhappy :) Motto: "When a new theory is
presented, no one believes it except the theorist. When new data is
presented, everyone believes it, except the person who prepared the
data." --- T. von Karman


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