finding trans-membrane domains of proteins

David Jones jones at bsm.biochemistry.ucl.ac.uk
Sun Apr 24 05:09:10 EST 1994


john f hess phd (jfhess at ucdavis.edu) wrote:
> Howdy everyone, 

> This seems to be the place to ask this question. I am interested in
> programs that will analyze protein sequences and tell me where potential
> trans-membrane domains are. 

> I am currently using MacDNAsis on my mac and have GCG on a vax on main
> campus. If a shareware program is available at indiana or ? please let me
> know. Alternatively, I can check the rest of UCD for some other
> commercially available program that does what I want.

A PC executable version of our transmembrane protein prediction program
MEMSAT is available via anonymous FTP from ftp.biochem.ucl.ac.uk
(128.40.46.11) - download the files in pub/MEMSAT. It's also available
from the EMBL file server. This program implements a new method we have
developed to not only accurately locate tm regions, but to work out the
optimum topology (i.e. whether each tm points into or out of the membrane)
as well (see Biochemistry vol 33 p3048 for details). The C source code is
available via e-mail (see the README file on ftp.biochem), and this should
compile on most platforms - though I haven't a Mac to try it on, VAX should
be OK. If anyone manages to compile it on a Mac I'd be interested to know.

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