Predicting novel RNA-RNA interactions

Curr Opin Struct Biol. 2008 Jun;18(3):387-93. doi: 10.1016/ Epub 2008 May 14.


The purpose of this article is to give a brief, yet concise overview of the current computational methods for predicting novel RNA-RNA interactions, that is interactions whose characteristic features we do not yet know. We start by briefly reviewing experimentally confirmed examples of RNA-RNA interactions before introducing computational methods for predicting RNA-RNA interactions. We will focus primarily on the interactions between different RNA molecules, that is trans RNA-RNA interactions, and will only discuss methods for predicting RNA structure, that is cis-only RNA-RNA interactions, where this helps to gain a better understanding. We conclude by discussing the merits of the different approaches and provide an outlook on probably and desirable future developments in the field.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Models, Molecular
  • Nucleic Acid Conformation
  • RNA / chemistry*


  • RNA