The ARTS web server for aligning RNA tertiary structures

The ARTS web server for aligning RNA tertiary structures (2006)

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by Oranit Dror , Ruth Nussinov , Haim J. Wolfson

Venue:	Nucleic Acids Res
Citations:	35 - 0 self

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@ARTICLE{Dror06thearts,
    author = {Oranit Dror and Ruth Nussinov and Haim J. Wolfson},
    title = {The ARTS web server for aligning RNA tertiary structures},
    journal = {Nucleic Acids Res},
    year = {2006},
    pages = {412--415}
}

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Abstract

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 allagainst-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

Keyphrases

art web server rna tertiary structure web server priori unknown common substructure important task nucleic acid structure structural comparison small local motif rna molecule share similar functional property local contiguous tertiary motif tertiary structure successive base pair common structural feature current available tool partial solution nucleic acid rna community protein data bank allagainst-all comparison software package identified common substructure rna structure large global fold common substructure