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Nucleic Acids Research 2006 34(Web Server issue):W95-W98; doi:10.1093/nar/gkl264
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© 2006 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-commerical use, distribution, and reproduction in any medium, provided the original work is properly cited.

Article

OPAAS: a web server for optimal, permuted, and other alternative alignments of protein structures

Edward S. C. Shih, Ruei-chi R. Gan and Ming-Jing Hwang*

Institute of Biomedical Sciences, Academia Sinica Taipei 11529, Taiwan

*To whom correspondence should be addressed. Tel: +886 2 2789 9033; Fax: +886 2 2788 7641; Email: mjhwang{at}ibms.sinica.edu.tw

Received February 13, 2006. Revised March 4, 2006. Accepted March 31, 2006.

The large number of experimentally determined protein 3D structures is a rich resource for studying protein function and evolution, and protein structure comparison (PSC) is a key method for such studies. When comparing two protein structures, almost all currently available PSC servers report a single and sequential (i.e. topological) alignment, whereas the existence of good alternative alignments, including those involving permutations (i.e. non-sequential or non-topological alignments), is well known. We have recently developed a novel PSC method that can detect alternative alignments of statistical significance (alignment similarity P-value <10–5), including structural permutations at all levels of complexity. OPAAS, the server of this PSC method freely accessible at our website (http://opaas.ibms.sinica.edu.tw), provides an easy-to-read hierarchical layout of output to display detailed information on all of the significant alternative alignments detected. Because these alternative alignments can offer a more complete picture on the structural, evolutionary and functional relationship between two proteins, OPAAS can be used in structural bioinformatics research to gain additional insight that is not readily provided by existing PSC servers.


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