hello,
proper domain orientation can be imposed during modeling if you use the
the full structure , two domains, simultaneously. In this way
interdomain restraints will be derived from the template and applied to
your target.
Andras
Stefano Ciurli wrote:
>
> I have the following question:
> I wish to model a series of homologous proteins (28 in total) for
> which I have the structure of the first and the 26th in order of
> sequence homology (ranging from ca. 55% to ca. 20%). The protein is
> made of two domains. The two available structures are quite similar
> except for the orientation of one domain with respect to the other
> (significantly off). What is the best approach to model sequences #2
> to #25 and #27-#28??? Is there an accepted protocol in order to model
> multidomain proteins? I know that one of the biggest problems with
> modelling protein structures is encountered when you have more than
> one domain, that is, to model relative domain orientation. Is there a
> way out? How would you proceed using Modeller???
--
,
Andras Fiser, PhD # phone: (212) 327 7216
The Rockefeller University # fax: (212) 327 7540
Box 270, 1230 York Avenue # e-mail:
New York, NY 10021-6399, USA # http://salilab.org/~andras