BINDING FREE ENERGY CALCULATION VIA MOLECULAR DYNAMICS SIMULATIONS FOR A miRNA:mRNA INTERACTION

G. Paciello, A. Acquaviva, E. Ficarra, M. A. Deriu, A. Grosso, E. Macii

Abstract

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.

References

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Paper Citation


in Harvard Style

Paciello G., Acquaviva A., Ficarra E., A. Deriu M., Grosso A. and Macii E. (2011). BINDING FREE ENERGY CALCULATION VIA MOLECULAR DYNAMICS SIMULATIONS FOR A miRNA:mRNA INTERACTION . In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2011) ISBN 978-989-8425-36-2, pages 318-321. DOI: 10.5220/0003167703180321


in Bibtex Style

@conference{bioinformatics11,
author={G. Paciello and A. Acquaviva and E. Ficarra and M. A. Deriu and A. Grosso and E. Macii},
title={BINDING FREE ENERGY CALCULATION VIA MOLECULAR DYNAMICS SIMULATIONS FOR A miRNA:mRNA INTERACTION},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2011)},
year={2011},
pages={318-321},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0003167703180321},
isbn={978-989-8425-36-2},
}


in EndNote Style

TY - CONF
JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2011)
TI - BINDING FREE ENERGY CALCULATION VIA MOLECULAR DYNAMICS SIMULATIONS FOR A miRNA:mRNA INTERACTION
SN - 978-989-8425-36-2
AU - Paciello G.
AU - Acquaviva A.
AU - Ficarra E.
AU - A. Deriu M.
AU - Grosso A.
AU - Macii E.
PY - 2011
SP - 318
EP - 321
DO - 10.5220/0003167703180321