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




A novel method for predicting transmembrane segments in proteins based on a statistical analysis of the SwissProt database: the PRED-TMR algorithm - Download this document for free, or read online. Document in PDF available to download.

* Corresponding author 1 Biophysics and Bioinformatics Laboratory

Abstract : 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-

Keywords : hydrophobicity analysis membrane proteins prediction protein structure transmembrane regions





Author: Claude Pasquier - Vasilis Promponas - Giorgos Palaios - Ioannis Hamodrakas - Stavros Hamodrakas -

Source: https://hal.archives-ouvertes.fr/



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