Rapid membrane protein topology prediction
2011 (English)In: Bioinformatics, ISSN 1367-4803, E-ISSN 1460-2059, Vol. 27, no 9, 1322-1323 p.Article in journal (Refereed) Published
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.
Place, publisher, year, edition, pages
2011. Vol. 27, no 9, 1322-1323 p.
Bioinformatics and Systems Biology
Research subject Computing Science; Molecular Biotechnology
IdentifiersURN: urn:nbn:se:su:diva-61921DOI: 10.1093/bioinformatics/btr119ISI: 000290331600023OAI: oai:DiVA.org:su-61921DiVA: diva2:438639
FunderSwedish Research Council, VR-NT 2009-5072; VR-M 2007-3065EU, FP7, Seventh Framework Programme, 512092; 201924Swedish Foundation for Strategic Research