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Nucleic Acids Research Advance Access originally published online on October 18, 2007
Nucleic Acids Research 2008 36(Database issue):D392-D397; doi:10.1093/nar/gkm842
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Nucleic Acids Research, 2008, Vol. 36, Database issue D392-D397
© 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.

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

Articles

RNAJunction: a database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesign

Eckart Bindewald1, Robert Hayes2, Yaroslava G. Yingling2, Wojciech Kasprzak1 and Bruce A. Shapiro2,*

1Basic Research Program, SAIC-Frederick and 2Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702, USA

*To whom correspondence should be addressed. Tel: 301 846 5536; Fax: 301 846 5598; Email: bshapiro{at}ncifcrf.gov

Received August 14, 2007. Revised September 21, 2007. Accepted September 25, 2007.

We developed a database called RNAJunction that contains structure and sequence information for RNA structural elements such as helical junctions, internal loops, bulges and loop–loop interactions. Our database provides a user-friendly way of searching structural elements by PDB code, structural classification, sequence, keyword or inter-helix angles. In addition, the structural data was subjected to energy minimization. This database is useful for analyzing RNA structures as well as for designing novel RNA structures on a nanoscale. The database can be accessed at: http://rnajunction.abcc.ncifcrf.gov/


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