CCL: (re-)relaxing molecules

[chupvl <chupvl|,|gmail.com>]

 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>