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RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods

Volume 1097 of the series Methods in Molecular Biology pp 395-415

Date:

Automated Modeling of RNA 3D Structure

  • Kristian RotherAffiliated withLaboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology Email author 
  • , Magdalena RotherAffiliated withLaboratory of Bioinformatics, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University
  • , Pawel SkibaAffiliated withLaboratory of Bioinformatics, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University
  • , Janusz M. BujnickiAffiliated withLaboratory of Bioinformatics, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University

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Abstract

This chapter gives an overview over the current methods for automated modeling of RNA structures, with emphasis on template-based methods. The currently used approaches to RNA modeling are presented with a side view on the protein world, where many similar ideas have been used. Two main programs for automated template-based modeling are presented: ModeRNA assembling structures from fragments and MacroMoleculeBuilder performing a simulation to satisfy spatial restraints. Both approaches have in common that they require an alignment of the target sequence to a known RNA structure that is used as a modeling template. As a way to find promising template structures and to align the target and template sequences, we propose a pipeline combining the ParAlign and Infernal programs on RNA family data from Rfam. We also briefly summarize template-free methods for RNA 3D structure prediction. Typically, RNA structures generated by automated modeling methods require local or global optimization. Thus, we also discuss methods that can be used for local or global refinement of RNA structures.

Key words

RNA structure Structure prediction Homology modeling Comparative modeling De novo modeling Template search Structure refinement