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Protein Engineering, Vol. 14, No. 6, 387-390, June 2001
© 2001 Oxford University Press

COMMUNICATION

A novel tool for the prediction of transmembrane protein topology based on a statistical analysis of the SwissProt database: the OrienTM algorithm

Theodore D. Liakopoulos, Claude Pasquier and Stavros J. Hamodrakas1,

Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, Athens 157 01, Greece

OrienTM is a computer software that utilizes an initial definition of transmembrane segments to predict the topology of transmembrane proteins from their sequence. It uses position-specific statistical information for amino acid residues which belong to putative non-transmembrane segments derived from statistical analysis of non-transmembrane regions of membrane proteins stored in the SwissProt database. Its accuracy compares well with that of other popular existing methods. A web-based version of OrienTM is publicly available at the address http://biophysics.biol.uoa.gr/OrienTM.


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