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Re: the alignment problem

In message <>
   Margot Ernst writes:
> Hi Modeller developers and friends,
> in Sanchez and Sali 1997 Curr Opin Struct Biol 7:206-214
> I read that a possible way to improve on homology modeling below 30 PID could
> be "iterative changes in the alignment during caluclation"
> My question is: Is this a great idea that has been realized already and I
>  just missed where and how, is it work in progress or has it been discarded
>  again due to technical problems?

I believe this iterative approach to homology modelling
is used routinely.  See for example Burke et al (1999),
Proteins Suppl 3:55-60.  A three-dimensional alignment of
a model with the template(s) is made, and the implied
linear alignment is adjusted so as to preserve local
structural features that might be expected to be
conserved. The new alignment is then used to build an
improved model, and so on.

I do not know whether the full procedure has been
automated successfully.


Paul Davis