How to predict transmembrane protein topology?

[Mike Mitchell]

In article <44efok$jf8 at fu-berlin.de>, strecker at chemie.fu-berlin.de
(Andreas Strecker) wrote:

> In article <4486ld$dpu at news.ust.hk>, bclong at uxmail.ust.hk (Terence) wrote:
> >
> >       Hello.
> >
> >       I often read in journals that a certain transmembrane topology is
> >determined/predicted for a certain transmemnrane protein. How is this done?
> >Is this done thru some commercial/public domain software? Or is it just by
> >eyeballing how many hydrophobic segment there? 
> 
> Hi Terence!
> 
> There are a number of transmembrane topology prediction algorithms, none of 
> which is very reliable - for a review see Fasman & Gilbert, TIBS 15 (1990), 
> pp. 89-92 and a contradicting opinion in the same TIBS issue by Jaehnig, TIBS 
> 15 (1990), pp. 93-95. You will find citations for the algorithms in the first 
> paper. Generally speaking, results for the prediction of transmembrane 
> peptides are difficult to assess since there are only few crystal structures 
> available for these domains. Hope this helps, check out the two papers.
> 
> Andreas

There is also a Mac application called TopPred II that predicts and displays
the topology of transmembrane regions. M.G. Claros and G. von Heijne, CABIOS
10(6), 685-686 (1994). It is avaliable by ftp from ...

   ftp://ftp.ebi.ac.uk/pub/software/mac/TopPredII.hqx

   ftp://ftp.bio.indianna.edu/molbio/mac/toppred12.hqx

and from the author, Manual G. Cloros (claros at biolgie.ens.fr)