From owner-chemistry@ccl.net Sat Oct 13 08:36:00 2007
From: "chupvl chupvl~!~gmail.com" <owner-chemistry:server.ccl.net>
To: CCL
Subject: CCL: (re-)relaxing molecules
Message-Id: <-35377-071013082629-21724-XaFf6Z8WQoRk3hqJkLYt4w:server.ccl.net>
X-Original-From: chupvl <chupvl|,|gmail.com>
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Date: Sat, 13 Oct 2007 15:26:35 +0400
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Sent to CCL by: chupvl [chupvl|gmail.com]
Hello!

In my point there three main ways of 3D alignment of the molecules

- point-2-point matching as in MATCH potion of Sybyl
- pharmacophoric matching
- receptor-based alignment (You'll be using MATCH option after docking 
of series of molecules)

and one more (I don't met an article about this but I think it's exist - 
is molecular descriptors alignment after descriptors selection based eg 
on good QSAR model)

Vladimir Chupakhin
MSU, Dpt. of Chemistry,
Moscow, Russia



aps1968**googlemail.com wrote:
> Sent to CCL by: aps1968*|*googlemail.com
> Dear CClrs,
>
> in order to perform CoMFA computations in Sybyl, I aligned my already
> externally optimized molecules with the use of the function MATCH, taking
> into account the fragment common for all molecules. The referee of the paper
> however asks if the molecules were re-relaxed after the MATCH procedure.
> I am not quite sure I understand what he means. Should I again in the
> new positions perform any further optimization? They are already
> optimized. He also
> suggests a pharmacofore based alignment prior to comfa and again asks to
> consider relaxing the conformers after MATCH alignment prior to comfa.
> Any comments to that? Which alternative alignment methods can be
> recommended to a SYBYL user?
>
> Regards,
>
> Andy>
>
>
>
>