TOPCONS Friday, July 30 2010
Main Menu
New query
SCAMPI
OCTOPUS
ΔG-scale
ZPRED
PRO/PRODIV
Download
Help

Consensus prediction of membrane protein topology
 
For large benchmark sets and full proteome scans, use the SCAMPI 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
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