Nucleic Acids Research Advance Access originally published online on October 8, 2008
Nucleic Acids Research 2009 37(Database issue):D315-D322; doi:10.1093/nar/gkn675
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Nucleic Acids Research, 2009, Vol. 37, Database issue D315-D322
© 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]
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CC+: a relational database of coiled-coil structures
1School of Chemistry, University of Bristol, Bristol BS8 1TS and 2Department of Biochemistry, School of Medical Sciences, University Walk, Bristol BS8 1TD, UK
*To whom correspondence should be addressed. Tel: +44 (0)117 95 46347; Fax: +44 (0)117 929 8611; Email: d.n.woolfson{at}bristol.ac.uk
Received August 15, 2008. Revised September 22, 2008. Accepted September 22, 2008.
We introduce the CC+ Database, a detailed, searchable repository of coiled-coil assignments, which is freely available at http://coiledcoils.chm.bris.ac.uk/ccplus. Coiled coils were identified using the program SOCKET, which locates coiled coils based on knobs-into-holes packing of side chains between 
-helices. A method for determining the overall sequence identity of coiled-coil sequences was introduced to reduce statistical bias inherent in coiled-coil data sets. There are two points of entry into the CC+ Database: the ‘Periodic Table of Coiled-coil Structures’, which presents a graphical path through coiled-coil space based on manually validated data, and the ‘Dynamic Interface’, which allows queries of the database at different levels of complexity and detail. The latter entry level, which is the focus of this article, enables the efficient and rapid compilation of subsets of coiled-coil structures. These can be created and interrogated with increasingly sophisticated pull-down, keyword and sequence-based searches to return detailed structural and sequence information. Also provided are means for outputting the retrieved coiled-coil data in various formats, including PyMOL and RasMol scripts, and Position-Specific Scoring Matrices (or amino-acid profiles), which may be used, for example, in protein-structure prediction.
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