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. 2008 Jan;36(Database issue):D392-7.
doi: 10.1093/nar/gkm842. Epub 2007 Oct 18.

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

Eckart Bindewald  1 , Robert Hayes, Yaroslava G Yingling, Wojciech Kasprzak, Bruce A Shapiro
Affiliations

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

Eckart Bindewald et al. Nucleic Acids Res. 2008 Jan.

Abstract

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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Figures

Figure 1.
Figure 1.
Schematic drawing of a three-way junction.
Figure 2.
Figure 2.
Schematic drawing of a kissing loop. Each circle represents one nucleotide; the single-stranded regions are indicated in gray.
Figure 3.
Figure 3.
Result page of an RNA loop–loop interaction derived from PDB structure 2BJ2.
See this image and copyright information in PMC

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