TOBMODEL Wednesday, October 24 2018
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C-alpha 3D Modelling of Transmembrane Beta barrel proteins.
TOBMODEL is ideal for generating low-resolution c-alpha 3D models for putative TMBs. TOBMODEL ranks the BOCTOPUS topologies and choses the top-ranked topology for Model generation.
TOBMODEL allows for requests of up to 1 protein sequence at a time for better predictive performance. If more than 1 protein sequences are input, only the first one is processed.
Please NOTE that due to limited resources we currently test only 5 topologies generated by BOCTOPUS.
Enter up to 1 protein sequences in FASTA format


Alternatively, upload a text file containing up to 1 protein sequences in FASTA format


      

 
References
BOCTOPUS:
BOCTOPUS: Improved topology prediction of transmembrane beta barrel proteins. Sikander Hayat and Arne Elofsson (2012)Bioinformatics 28(4), 516-522. [Pubmed]
OCTOPUS:
OCTOPUS: improving topology prediction by two-track ANN-based preference scores and an extended topological grammar. Håkan Viklund and Arne Elofsson (2008) Bioinformatics 24(15), 1662-1668. [Pubmed]
TOBMODEL:
TOBMODEL: Toward 3D modeling of transmembrane beta barrel proteins based on z-coordinate and topology prediction. Sikander Hayat and Arne Elofsson (ISMB 2012)
Full Atom model based on:
Gront, D., Kmiecik, S., and Kolinski, A. (2007). Backbone building from quadrilaterals: A fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinates. Journal of computational chemistry, 28(9), 1593-1597.
 
© 2011 Stockholm University, Stockholm Bioinformatics Centre, Center for Biomembrane Research