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. 2009 Jul;37(Web Server issue):W465-8.
doi: 10.1093/nar/gkp363. Epub 2009 May 8.

TOPCONS: consensus prediction of membrane protein topology

Andreas Bernsel  1 , Håkan Viklund, Aron Hennerdal, Arne Elofsson
Affiliations

TOPCONS: consensus prediction of membrane protein topology

Andreas Bernsel et al. Nucleic Acids Res. 2009 Jul.

Abstract

TOPCONS (http://topcons.net/) is a web server for consensus prediction of membrane protein topology. The underlying algorithm combines an arbitrary number of topology predictions into one consensus prediction and quantifies the reliability of the prediction based on the level of agreement between the underlying methods, both on the protein level and on the level of individual TM regions. Benchmarking the method shows that overall performance levels match the best available topology prediction methods, and for sequences with high reliability scores, performance is increased by approximately 10 percentage points. The web interface allows for constraining parts of the sequence to a known inside/outside location, and detailed results are displayed both graphically and in text format.

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Figures

Figure 1.
Figure 1.
TOPCONS workflow: four of the topology predictors make use of multiple sequence information and require a sequence profile as input, created using BLAST (18), whereas the fifth method (SCAMPI-single) only requires the protein sequence. The topology predictions are used to construct a topology profile, which is fed into the TOPCONS hidden Markov model.
Figure 2.
Figure 2.
Estimated probability of correct topology prediction as a function of reliability score. Of the sequences in the benchmark set, 71% have a reliability score >70, and among those, 93% of the predictions are correct. The probability of a correct topology prediction (y-axis) was estimated as the prediction accuracy among proteins with reliability score ± 10 from the value given by the x-axis.
Figure 3.
Figure 3.
Example output from the TOPCONS webserver, based on the Bacteriorhodopsin sequence from Halobacterium species (SwissProt-ID: BACR_HALS4). (A) Topologies predicted by the individual methods, predicted Z-coordinates, and predicted ΔG-values across the sequence. (B) The consensus prediction, which is based on the individual methods, and reliability score across the sequence.
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