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Nucleic Acids Research Advance Access originally published online on May 15, 2008
Nucleic Acids Research 2008 36(Web Server issue):W202-W209; doi:10.1093/nar/gkn255
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Nucleic Acids Research, 2008, Vol. 36, No. suppl_2 W202-W209
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Articles

PROTEUS2: a web server for comprehensive protein structure prediction and structure-based annotation

Scott Montgomerie1, Joseph A. Cruz1, Savita Shrivastava1, David Arndt1, Mark Berjanskii1 and David S. Wishart1,2,*

1Department of Computing Science and Department of Biological Sciences, University of Alberta and 2National Research Council, National Institute for Nanotechnology (NINT), Edmonton, AB, Canada T6G 2E8

*To whom correspondence should be addressed. Tel: +780 492 0383; Fax: +780 492 5305; Email: david.wishart{at}ualberta.ca

Received February 1, 2008. Revised April 12, 2008. Accepted April 20, 2008.

PROTEUS2 is a web server designed to support comprehensive protein structure prediction and structure-based annotation. PROTEUS2 accepts either single sequences (for directed studies) or multiple sequences (for whole proteome annotation) and predicts the secondary and, if possible, tertiary structure of the query protein(s). Unlike most other tools or servers, PROTEUS2 bundles signal peptide identification, transmembrane helix prediction, transmembrane β-strand prediction, secondary structure prediction (for soluble proteins) and homology modeling (i.e. 3D structure generation) into a single prediction pipeline. Using a combination of progressive multi-sequence alignment, structure-based mapping, hidden Markov models, multi-component neural nets and up-to-date databases of known secondary structure assignments, PROTEUS is able to achieve among the highest reported levels of predictive accuracy for signal peptides (Q2 = 94%), membrane spanning helices (Q2 = 87%) and secondary structure (Q3 score of 81.3%). PROTEUS2's homology modeling services also provide high quality 3D models that compare favorably with those generated by SWISS-MODEL and 3D JigSaw (within 0.2 Å RMSD). The average PROTEUS2 prediction takes ~3 min per query sequence. The PROTEUS2 server along with source code for many of its modules is accessible a http://wishart.biology.ualberta.ca/proteus2.


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