TOPCONS Friday, July 25 2014
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Consensus prediction of membrane protein topology
 
For large benchmark sets and full proteome scans, use the SCAMPI server or the TOPCONS-single server instead.

Enter one amino acid sequence in FASTA format

Restrainment options
Restrain parts of the sequence to a known Inside/Outside/Membrane location
N-term  (Optional)
C-term  (Optional)
Other  (Optional)
 String of one or more entries with format [first]-[last]-[label]; where [first] is first residue and [last] is last residue in restrained range, and [label] is i (Inside), o (Outside) or M (Membrane). Example: 1-1-o;20-25-M;

      

 
References
TOPCONS:
TOPCONS: consensus prediction of membrane protein topology. Andreas Bernsel, Håkan Viklund, Aron Hennerdal and Arne Elofsson (2009) Nucleic Acids Research 37(Webserver issue), W465-8 [PubMed]
SCAMPI:
Prediction of membrane-protein topology from first principles. Andreas Bernsel, Håkan Viklund, Jenny Falk, Erik Lindahl, Gunnar von Heijne and Arne Elofsson (2008) Proc. Natl. Acad. Sci. USA. 105, 7177-7181. [Pubmed]
OCTOPUS:
A method that improves topology prediction for transmembrane proteins by using two-track ANN-based preference scores and an improved topological grammar. Håkan Viklund and Arne Elofsson (2008) Bioinformatics. 24, 1662-1668. [Pubmed]
ΔG-scale:
Molecular code for transmembrane-helix recognition by the Sec61 translocon. Tara Hessa, Nadja Meindl-Beinker, Andreas Bernsel, Joy Kim, Yoko Sato, Mirjam Lerch, Carolina Lundin, IngMarie Nilsson, Stephen H. White, and Gunnar von Heijne (2007) Nature 450, 1026-1030. [PubMed]
ZPRED:
ZPRED: Predicting the distance to the membrane center for residues in alpha-helical membrane proteins. Erik Granseth, Håkan Viklund and Arne Elofsson (2006) Bioinformatics 22, e191-e196 [PubMed]
PRO/PRODIV-TMHMM:
Best alpha-helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information. Håkan Viklund and Arne Elofsson (2004) Protein Science 13, 1908-1917 [PubMed]
 
© 2008 Stockholm University, Stockholm Bioinformatics Center