Rapid membrane protein topology prediction

Bioinformatics. 2011 May 1;27(9):1322-3. doi: 10.1093/bioinformatics/btr119.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Internet*
  • Markov Chains
  • Membrane Proteins / chemistry*
  • Protein Structure, Secondary*
  • Sequence Alignment
  • Sequence Analysis, Protein / methods*
  • Software*


  • Membrane Proteins