transmembrane region prediction

khofmann at biomed.biolan.uni-koeln.de khofmann at biomed.biolan.uni-koeln.de
Thu Jul 29 10:12:18 EST 1993


In article <1993Jul28.132216.105504 at embl-heidelberg.de> ouzounis at embl-heidelberg.de 
writes:

>Hi
>
>Does anybody know of a good program/algorithm that predicts transmembrane
>regions in protein sequences? I am looking for something more sophisticated
>than Kyte-Doolittle and similar hydrophobicity plots. Thanks.
>
>C A Ouzounis
>EMBL
>Heidelberg

I am currently working on a method for the prediction of transmembrane helices
using pattern of positional preferences of amino acids for particular regions
of the membrane spanning domain. The method seems to be more reliable than most
of the available algorithms although there are some pitfalls, too. 
As an additional advantage, this method also yields some information on the
most probable orientation of the transmembrane proteins.
I have written a (very crude) program applying the method, but it is not yet
ready for release. If someone is extremely interested, i am willing to send a
pre-version of the program (msdos only).

In the course of evaluating the above described method I tested most of the
the currently available programs. In my hands, the KKD-program in most cases
gave the best results (or the results i thought to be the best, since there 
isnot too much reliable testing material available).

The reference for the KKD-method is:

 P.Klein, M.Kanehisa and C.DeLisi: The detection and classification
 of membrane spanning proteins. Biochim. Biophys. Acta 815, 468-476 (1985)

There has been a short comparative review of TM-prediction methods in TIBS
somewhere in the 1990  issue (i don't have the reference at hand now). 
All programs reviewed therein (including the KKD-program) are available 
by FTP from VAX.WI.EDU

I hope this could be of help

best regards,
Kay.

 
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Kay O Hofmann                             Tel.: +49 221 478-6980
Institut fuer Biochemie (med. Fak.)       Fax.: +49 221 478-6979
Universitaet Koeln
Joseph Stelzmann Str. 52          Internet: khofmann at biomed.biolan.uni-koeln.de
D-50931 Koeln                               khofmann at gen1.genetik.uni-koeln.de
Germany
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