Orientation of TransMembrane proteins

Th.D. Liakopoulos, C.M. Pasquier and S.J. Hamodrakas Department of Cell Biology and Biophysics University of Athens

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 aminoacid residues which belong to putative non-transmembrane segments derived from a 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.

• Execute orienTM on a sequence

Additional information

The method was tested on

• a set of 72 proteins extracted from the set of the 101 non-homologous transmembrane proteins reported by Pasquier et al. (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, 12, 381-385), list available here.
• all transmembrane proteins of known topology of the SwissProt database (release 35)
• all transmembrane proteins of known topology of SwissProt (new entries in releases 36-39)
• the test set used to assess the accuracy of HMMTOP (J. Mol. Biol. 1998, 283, 489-506)
• the set of transmembrane proteins described by Moller et al. (Bioinformatics 2000, 16, 1159-60)

• A comparison of predictions for the set of '72' based on transmembrane segments (a) according to the SwissProt annotation ('observed') and (b) predicted by PRED-TMR ('predicted')
• and a length distribution of all transmembrane segments in SwissProt R35.

A paper describing our method has been published in Protein Engineering.

Our Database of non-transmembrane regions, DB-NTMR, can be accessed from here:

e-mail: liakop@biol.uoa.gr

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