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Bioinformatics 2005 21(Suppl 2):ii47-ii53; doi:10.1093/bioinformatics/bti1108
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oxfordjournals.org

ARTS: alignment of RNA tertiary structures

Oranit Dror 1,*, Ruth Nussinov 2,3 and Haim Wolfson 1

1School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University Tel Aviv 69978, Israel
2Sackler Institute of Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University Tel Aviv 69978, Israel
3Basic Research Program, SAIC-Frederick, Inc., Laboratory of Experimental and Computational Biology Building 469, Room 151, Frederick, MD 21702, USA

*To whom correspondence should be addressed.

Motivation: A fast growing number of non-coding RNAs have recently been discovered to play essential roles in many cellular processes. Similar to proteins, understanding the functions of these active RNAs requires methods for analyzing their tertiary structures. However, in contrast to the wide range of structure-based approaches available for proteins, there is still a lack of methods for studying RNA structures.

Results: We present a new computational method named ARTS (alignment of RNA tertiary structures). The method compares two nucleic acid structures (RNAs or DNAs) and detects a-priori unknown common substructures. These substructures can be either large global folds containing hundreds and even thousands of nucleotides or small local tertiary motifs with at least two successive base pairs. To the best of our knowledge, this is the first method of this type. The method is highly-efficient and was used to conduct an all-against-all comparison of all the RNA structures currently available in the Protein Data Bank.

Availability: The program, a web-server and supplementary information are available on http://bioinfo3d.cs.tau.ac.il/ARTS

Contact: oranit{at}post.tau.ac.il


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