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The ARTS web server for aligning RNA tertiary structures

  1. Author:
    Dror, O.
    Nussinov, R.
    Wolfson, H. J.

  2. Author Address

    Tel Aviv Univ, Raymond & Beverly Sackler Fac Exact Sci, Sch Comp Sci, IL-69978 Tel Aviv, Israel. Tel Aviv Univ, Sackler Fac Med, Sackler Inst Mol Med, IL-69978 Tel Aviv, Israel. NCI Frederick, Basic Res Program, SAIC Frederick, Ctr Canc Res,Neurobiol Program, Ft Detrick, MD 21702 USA.;Dror, O, Tel Aviv Univ, Raymond & Beverly Sackler Fac Exact Sci, Sch Comp Sci, IL-69978 Tel Aviv, Israel.;oranit@post.tau.ac.il
    1. Year: 2006
    2. Date: Jul
  2. Journal: Nucleic Acids Research
    1. 34
    2. Pages: W412-W415
  4. Type of Article: Article
  5. ISSN: 0305-1048
  1. 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 RNAandDNA). 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 downloadare freely accessible at http://bioinfo3d.cs.tau.ac.il/ARTS.

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  2. DOI: 10.1093/nar/gkl312
  3. View record in Web of Science®
  4. WOS: 000245650200083

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