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The HMMTOP server

HMMTOP is an automatic server for predicting transmembrane helices and topology of proteins, developed by G.E. Tusnády, at the Institute of Enzymology.
The method used by this prediction server is described in "G.E Tusnády and I. Simon (1998) Principles Governing Amino Acid Composition of Integral Membrane Proteins: Applications to Topology Prediction." J. Mol. Biol. 283, 489-506 (JMB) (Medline) (PDF).
The new features of HMMTOP 2.0 version is described in "G.E Tusnády and I. Simon (2001) The HMMTOP transmembrane topology prediction server" Bioinformatics 17, 849-850 (Bioinformatics) (Medline) (PDF).