A novel method for predicting transmembrane segments in proteins based on a statistical analysis of the SwissProt database: the PRED-TMR algorithm

Claude Pasquier (1) , Vasilis Promponas (1) , Giorgos A. Palaios (1) , J.S Hamodrakas (1) , Stavros J. Hamodrakas (1)

1 NKUA - National and Kapodistrian University of Athens

We present a novel method that predicts transmembrane domains in proteins using solely information contained in the sequence itself. The PRED-TMR algorithm described, refines a standard hydrophobicity analysis with a detection of potential termini ('edges', starts and ends) of transmembrane regions. This allows one both to discard highly hydrophobic regions not delimited by clear start and end configurations and to confirm putative transmembrane segments not distinguishable by their hydrophobic composition. The accuracy obtained on a test set of 101 non-homologous transmembrane proteins with reliable topologies compares well with that of other popular existing methods. Only a slight decrease in prediction accuracy was observed when the algorithm was applied to all transmembrane proteins of the SwissProt database (release 35). A WWW server running the PRED-TMR algorithm is available at http://o2.db.uoa. gr/PRED-TMR/

Mots clés: Protein structure prediction

Domaines: Bio-informatique [q-bio.QM]

Claude Pasquier, Vasilis Promponas, Giorgos A. Palaios, J.S Hamodrakas, Stavros J. Hamodrakas. A novel method for predicting transmembrane segments in proteins based on a statistical analysis of the SwissProt database: the PRED-TMR algorithm. Protein Engineering, Design and Selection, 1999, 12 (5), pp.381-5. ⟨hal-00170724v3⟩