New metrics for comparing and assessing discrepancies between RNA 3D structures and models

  1. Marc Parisien1,3,
  2. José Almeida Cruz2,3,
  3. Éric Westhof2 and
  4. François Major1
  1. 1Institute for Research in Immunology and Cancer, Department of Computer Science and Operations Research, Université de Montréal, Montréal, Québec H3C 3J7, Canada
  2. 2Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, 67084 Strasbourg Cedex, France
    1. 3 These authors contributed equally to this work.

    Abstract

    To benchmark progress made in RNA three-dimensional modeling and assess newly developed techniques, reliable and meaningful comparison metrics and associated tools are necessary. Generally, the average root-mean-square deviations (RMSDs) are quoted. However, RMSD can be misleading since errors are spread over the whole molecule and do not account for the specificity of RNA base interactions. Here, we introduce two new metrics that are particularly suitable to RNAs: the deformation index and deformation profile. The deformation index is calibrated by the interaction network fidelity, which considers base–base-stacking and base–base-pairing interactions within the target structure. The deformation profile highlights dissimilarities between structures at the nucleotide scale for both intradomain and interdomain interactions. Our results show that there is little correlation between RMSD and interaction network fidelity. The deformation profile is a tool that allows for rapid assessment of the origins of discrepancies.

    Keywords

    Footnotes

    • Reprint requests to: François Major, Institute for Research in Immunology and Cancer, Department of Computer Science and Operations Research, Université de Montréal, Montréal, Québec H3C 3J7, Canada; e-mail: major{at}iro.umontreal.ca; fax: (514) 343-5839; or Eric Westhof, Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 Rue René Descartes, 67084 Strasbourg Cedex, France; e-mail: E.Westhof{at}ibmc.u-strasbg.fr; fax: +33 (0)-3-88-41-70-46.

    • Article published online ahead of print. Article and publication date are at http://www.rnajournal.org/cgi/doi/10.1261/rna.1700409.

      • Received April 23, 2009.
      • Accepted July 10, 2009.
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