Automated Modeling of RNA 3D Structure

  • Kristian Rother
  • Magdalena Rother
  • Pawel Skiba
  • Janusz M. Bujnicki
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1097)

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 

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Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  • Kristian Rother
    • 1
  • Magdalena Rother
    • 2
  • Pawel Skiba
    • 2
  • Janusz M. Bujnicki
    • 2
  1. 1.Laboratory of Bioinformatics and Protein EngineeringInternational Institute of Molecular and Cell BiologyWarsawPoland
  2. 2.Laboratory of Bioinformatics, Faculty of Biology, Institute of Molecular Biology and BiotechnologyAdam Mickiewicz UniversityPoznanPoland

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