title: Rapid membrane protein topology prediction.
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.
  
  
  METHODS
  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.
authors.affiliation: Department of Biochemistry and Biophysics, Stockholm Bioinformatics Center, Center for Biomembrane Research, Swedish e-science Research Center, Stockholm University, Stockholm, Sweden.
authors.forename: Aron
authors.initials: A
authors.lastname: Hennerdal
authors.forename: Arne
authors.initials: A
authors.lastname: Elofsson
mesh_terms: D000465:Algorithms; D020407:Internet; D008390:Markov Chains; D008565:Membrane Proteins / Q000737:chemistry*; D017433:Protein Structure, Secondary; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software
chemical_list: D008565:Membrane Proteins