modeling helix bundles

Simon Andrews simon.andrews at bbsrc.ac.uk
Mon Jul 9 09:32:24 EST 2001


Mario Garcia wrote:
> 
> Dear all,
> We would need to predict by computer modeling the structure of
> the transmembrane domain of a channel protein likely to be composed by
> a 6 parallel helix bundle. Could anyone give us any advice or suggestion
> regarding methods and software specifically devoted on this subject? Any
> help will be welcome.

6TM?  Definitely not one of the large family of 7TM proteins?  There are
a couple of ways of modeling 7TM bundles, but I'm not sure how well
these will extrapolate to 6TM.

The pants way (definitely 7TM only):

	http://www.expasy.ch/cgi-bin/sm-gpcr.pl

The real way (may be able to be extended to 6TM - but probably not!):

	http://www.ysbl.york.ac.uk/~pavel/gpcr/7tm_1.html


Hope this helped?

Simon.




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