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Nucleic Acids Research Advance Access originally published online on October 8, 2008
Nucleic Acids Research 2009 37(Database issue):D328-D332; doi:10.1093/nar/gkn679
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Nucleic Acids Research, 2009, Vol. 37, Database issue D328-D332
© 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.

This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]

Articles

CPDB: a database of circular permutation in proteins

Wei-Cheng Lo, Chi-Ching Lee, Che-Yu Lee and Ping-Chiang Lyu*

Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 30013, Taiwan

*To whom correspondence should be addressed. Tel: +886 3 5742762; Fax: +886 3 5715934; Email: lslpc{at}life.nthu.edu.tw

Received August 13, 2008. Revised September 22, 2008. Accepted September 23, 2008.

Circular permutation (CP) in a protein can be considered as if its sequence were circularized followed by a creation of termini at a new location. Since the first observation of CP in 1979, a substantial number of studies have concluded that circular permutants (CPs) usually retain native structures and functions, sometimes with increased stability or functional diversity. Although this interesting property has made CP useful in many protein engineering and folding researches, large-scale collections of CP-related information were not available until this study. Here we describe CPDB, the first CP DataBase. The organizational principle of CPDB is a hierarchical categorization in which pairs of circular permutants are grouped into CP clusters, which are further grouped into folds and in turn classes. Additions to CPDB include a useful set of tools and resources for the identification, characterization, comparison and visualization of CP. Besides, several viable CP site prediction methods are implemented and assessed in CPDB. This database can be useful in protein folding and evolution studies, the discovery of novel protein structural and functional relationships, and facilitating the production of new CPs with unique biotechnical or industrial interests. The CPDB database can be accessed at http://sarst.life.nthu.edu.tw/cpdb


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