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Nucleic Acids Research 2006 34(Web Server issue):W412-W415; doi:10.1093/nar/gkl312
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© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Article

The ARTS web server for aligning RNA tertiary structures

Oranit Dror*, Ruth Nussinov1,2 and Haim J. Wolfson

School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University Tel Aviv 69978, Israel 1 Sackler Inst. of Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University Tel Aviv 69978, Israel 2 Basic Research Program, SAIC-Frederick, Center for Cancer Research, Nanobiology Program NCI-Frederick, Building 469, Room 151, Frederick, MD 21702, USA

*To whom correspondence should be addressed. Tel: +972-3-640 5395; Fax: +972-3-640 6476; Email: oranit{at}post.tau.ac.il

Received February 14, 2006. Revised March 6, 2006. Accepted April 11, 2006.

RNA molecules with common structural features may share similar functional properties. Structural comparison of RNAs and detection of common substructures is, thus, a highly important task. Nevertheless, the current available tools in the RNA community provide only a partial solution, since they either work at the 2D level or are suitable for detecting predefined or local contiguous tertiary motifs only. Here, we describe a web server built around ARTS, a method for aligning tertiary structures of nucleic acids (both RNA and DNA). ARTS receives a pair of 3D nucleic acid structures and searches for a priori unknown common substructures. The search is truly 3D and irrespective of the order of the nucleotides on the chain. The identified common substructures can be large global folds with hundreds and even thousands of nucleotides as well as small local motifs with at least two successive base pairs. The method is highly efficient and has been used to conduct an all-against-all comparison of all the RNA structures in the Protein Data Bank. The web server together with a software package for download are freely accessible at http://bioinfo3d.cs.tau.ac.il/ARTS.


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