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 follwing was copied from their server.
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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).
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Hope this can be of any help.
Mads Noerregaard-Madsen
Dept. Mol. Biol.
Odense University
Denmark
