Predicting structure and stability for RNA complexes with intermolecular loop-loop base-pairing.RNA loop-loop interactions are essential for genomic RNA dimerization and regulation of gene expression.  In this article, a statistical mechanics-based computational method that predicts the structures and thermodynamic stabilities of RNA complexes with loop-loop kissing interactions is described.  Benchmark tests with several experimentally validated systems show that the inclusion of the entropy parameters can indeed improve predictions for RNA complexes.  Furthermore, the method can predict not only the native structures of RNA/RNA complexes but also alternative metastable structures.  For instance, the model predicts that the SL1 domain of HIV-1 RNA can form two different dimer structures with similar stabilities. 
RNA
Furthermore, the method can predict not only the native structures of RNA/RNA complexes but also alternative metastable structures. 
RNA/RNA complexes
In this article, a statistical mechanics-based computational method that predicts the structures and thermodynamic stabilities of RNA complexes with loop-loop kissing interactions is described. 
computational method
In this article, a statistical mechanics-based computational method that predicts the structures and thermodynamic stabilities of RNA complexes with loop-loop kissing interactions is described. 
statistical mechanics-based computational method