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Nucleic Acids Research Advance Access published online on May 3, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm251
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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.

Computational Biology

LOMETS: A local meta-threading-server for protein structure prediction

Sitao Wu and Yang Zhang*

Center for Bioinformatics and Department of Molecular Bioscience, University of Kansas, 2030 Becker Dr, Lawrence, KS 6604, USA

*To whom correspondence should be addressed. Tel: +1 785 864 1948; Fax: +1 785 864 5558; Email: yzhang{at}ku.edu

Received December 22, 2006. Revised April 4, 2007. Accepted April 5, 2007.

We developed LOMETS, a local threading meta-server, for quick and automated predictions of protein tertiary structures and spatial constraints. Nine state-of-the-art threading programs are installed and run in a local computer cluster, which ensure the quick generation of initial threading alignments compared with traditional remote-server-based meta-servers. Consensus models are generated from the top predictions of the component-threading servers, which are at least 7% more accurate than the best individual servers based on TM-score at a t-test significance level of 0.1%. Moreover, side-chain and C-alpha (C{alpha}) contacts of 42 and 61% accuracy respectively, as well as long- and short-range distant maps, are automatically constructed from the threading alignments. These data can be easily used as constraints to guide the ab initio procedures such as TASSER for further protein tertiary structure modeling. The LOMETS server is freely available to the academic community at http://zhang.bioinformatics.ku.edu/LOMETS.


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