Ensemble Calc compute the final concentrations of miRNA and mRNA, and the net free energy change () of interaction. Ensemble Calc script computes equilibrium concentrations and free energy change when an oligo(ribo)nucleotide binds to a target nucleic acid. Although written for a specific application, the binding of a miRNA to a mRNA, it can be used for the binding of a short DNA oligo to a long(er) DNA target.
Chikako Ragan ; Professor Michael Zuker
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Chikako Ragan, Michael Zuker & Mark A. Ragan
Quantitative prediction of miRNA-mRNA interaction based on equilibrium concentrations
PLoS Computational Biology (February 2011)