Mads Noerregaard-Madsen mnm at BIOBASE.DK
Sun Aug 11 10:21:04 EST 1996

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.

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

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