Article

Rapid membrane protein topology prediction.

Department of Biochemistry and Biophysics, Stockholm Bioinformatics Center, Center for Biomembrane Research, Swedish e-science Research Center, Stockholm University, Stockholm, Sweden.
Bioinformatics (Impact Factor: 5.47). 05/2011; 27(9):1322-3. DOI: 10.1093/bioinformatics/btr119
Source: PubMed

ABSTRACT State-of-the-art methods for topology of α-helical membrane proteins are based on the use of time-consuming multiple sequence alignments obtained from PSI-BLAST or other sources. Here, we examine if it is possible to use the consensus of topology prediction methods that are based on single sequences to obtain a similar accuracy as the more accurate multiple sequence-based methods. Here, we show that TOPCONS-single performs better than any of the other topology prediction methods tested here, but ~6% worse than the best method that is utilizing multiple sequence alignments. AVAILABILITY AND IMPLEMENTATION: TOPCONS-single is available as a web server from http://single.topcons.net/ and is also included for local installation from the web site. In addition, consensus-based topology predictions for the entire international protein index (IPI) is available from the web server and will be updated at regular intervals.

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