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.


Additional information

OrienTM was trained on all transmembrane proteins of known topology of the SwissProt database (release 35).

The method was tested on

Test set

No of proteins

Topology correctly predicted by orienTM

Set of '72'

Eukaryotic

38

37 (97%) *

Prokaryotic

34

33 (97%) *

Subset of SwissProt (Release 35) with known topology
(TRAINING SET)

Eukaryotic

3240

3080 (95%)

Prokaryotic

451

392 (87%)

Subset of SwissProt (new entries in Releases 36-39) with known topology

Eukaryotic

588

550 (94%)

Prokaryotic

99

86 (87%)

HMMTOP test set

TSs predicted by HMMTOP

158

144 (89%)

TSs taken from SwissProt annotations

158

149 (94%)

Moller et al.

Set A

24

22 (92%)

Non redundant set

121

107 (88%)

* OrienTM fails on the proteins TRSR_HUMAN and CYOA_ECOLI (SwissProt codes)

See also

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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