Version 1.0

A novel method for predicting transmembrane segment in proteins based on a statistical analysis of the SwissProt database

Pasquier, C., Promponas, V.J., Palaios, G.A., Hamodrakas, J.S. and Hamodrakas, S.J.
Department of Cell Biology and Biophysics,
Faculty of Biology, University of Athens
Panepistimiopolis, Kouponia, Athens 15701, Greece

PRED-TMR is a novel method that predicts transmembrane domains in proteins using solely information contained in the sequence itself. The algorithm refines a standard hydrophobicity analysis with a detection of potential termini ("edges", starts and ends) of transmembrane regions. This allows 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 transmembranes 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).

The algorithm is described in :

Pasquier C, Promponas VJ, Palaios GA, Hamodrakas JS, Hamodrakas SJ:
A novel method for predicting transmembrane segments in proteins based on a statistical analysis of the SwissProt database: the PRED-TMR algorithm. Protein Eng 1999 May;12(5):381-5

Now, you can :

Run PRED-TMR on a sequence

Browse the results obtained with the algorithm

View additional and not yet published material

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Claude Pasquier