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Nucleic Acids Research Advance Access published online on June 21, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm319
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© 2007 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.

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Pcons.net: protein structure prediction meta server

Björn Wallner1,*, Per Larsson2 and Arne Elofsson2

1Department of Biochemistry, University of Washington, Box 357350, Seattle, WA 98195, USA and 2Center for Biomembrane Research, Stockholm University, SE-106 91 Stockholm, Sweden

*To whom correspondence should be addressed. Tel: +1 206 616 4396; Fax: +1 206 685 1792; Email: bjornwa{at}u.washington.edu

Received January 26, 2007. Revised March 19, 2007. Accepted April 17, 2007.

The Pcons.net Meta Server (http://pcons.net) provides improved automated tools for protein structure prediction and analysis using consensus. It essentially implements all the steps necessary to produce a high quality model of a protein. The whole process is fully automated and a potential user only submits the protein sequence. For PSI-BLAST detectable targets, an accurate model is generated within minutes of submission. For more difficult targets the sequence is automatically submitted to publicly available fold-recognition servers that use more advanced approaches to find distant structural homologs. The results from these servers are analyzed and assessed for structural correctness using Pcons and ProQ; and the user is presented with a ranked list of possible models. In addition, if the protein sequence contains more than one domain, these are automatically parsed out and resubmitted to the server as individual queries.


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