Wonderful membrane topology

Jessica Boyd jboyd at acs.ucalgary.ca
Tue Jun 24 14:20:47 EST 1997

In article <l03020900afd3db7cff3f@[]>, Saisu at mcb.liu.se
(Sailesh Surapureddi) wrote:

> Hi Everybody
>         Everytime a new protein is published, usually a nice  picture is
> included  predicting the membrane topology basing on the hydropathy
> analysis. I have been breaking my head to figure out how they do it. I have
> all these kinds of hydropathy plots for a protein (Kyte & Doolittle, Rose &
> Roy, ie what ever I could from the MacDnasis program) but still cant come
> up with a picture.
>         Is there any program out there which arranges all the amino acids,
> going  thru the membranes, nicely curling and folding..if you happen to
> know any such program or have experience in arranging the aminoacids in
> predicting its topology, I would like to hear from you and request your
> kind help in solving my protein topology.
> appreciate your kind help in advance
> Sailesh.

There are two topology prediction programs that I have found usefull. 
TopPredII is Shareware that can be downloaded from many anonomous FTP
sites, it is fairly easy to use and supplies some graphic images of the
TMPred is an InterNet based program on the Baylor College of Medicine
(BCM) molecular biology web page  (a very good page by the way), it may be
more accurate, but has no graphics.  Both of these programs use the
hydrophathy profile and some other interesting bits of data (location of
positively charged residues, prediction of a-helices, the type of
membrane, etc) to predict the structure.  

If you want pretty pictures with all the amino acids swirling around
inside the membrane, you will have to draw it yourself with a
wordprocessor or a drawing program.  I don't know of any programs that
make it easier for you. 

Good Luck
Jessica Boyd

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