oops, something got lost in the mail - sorry.
I don't know about TOPPRED, but the PredictProtein server at EMBL can
perhaps be of help to you.
http://www.embl-heidelberg.de/predictprotein/predictprotein.html
The following was copied from their server.
Refined prediction of transmembrane helices and topology (PHDtopology;
examples for: request; and output)
The neural network prediction of transmembrane helices (PHDhtm) is
refined by a dynamic programming-like algorithm. This method resulted in
correct predictions of all transmembrane helices for 89% of the 131
proteins used in a cross-validation test; more than 98% of the
transmembrane helices were correctly predicted. The output of this
method is used to predict topology, i.e., the orientation of the N-term
with respect to the membrane. The expected accuracy of the topology
prediction is > 86%. Prediction accuracy is higher than average for
eukaryotic proteins and lower than average for prokaryotes. PHDtopology
is more accurate than all other methods tested on identical data sets
(Rost, Casadio & Fariselli, 1996a and 1996b; evaluation of accuracy).
Hope this can be of any help.
Mads Noerregaard-Madsen
Dept. Mol. Biol.
Odense University
Denmark
