In this paper we present a methodology to evaluate the binding free energy of a miRNA-mRNA complex through Molecular Dynamics-Thermodynamic Integration simulations. We applied our method on the C-elegans let-7 miRNA:lin-41 mRNA complex, known to be a validate miRNA:mRNA interaction, in order to evaluate the energetic stability of the structure. The methodology has been designed to face the various challenges of nucleic acid simulations and binding free energy computations and to allow an optimal trade-off between accuracy and computational cost.
Binding free energy calculation via molecular dynamics simulations for a miRNA:mRNA interaction / Paciello, G.; Acquaviva, A.; Ficarra, E.; Deriu, M. A.; Grosso, A.; Macii, E.. - (2011), pp. 318-321. (Intervento presentato al convegno International Conference on Bioinformatics Models, Methods and Algorithms, BIOINFORMATICS 2011 tenutosi a Rome, ita nel JAN 26-29, 2011).