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Authors: G. Paciello ; A. Acquaviva ; E. Ficarra ; M. A. Deriu ; A. Grosso and E. Macii

Affiliation: Politecnico di Torino, Italy

ISBN: 978-989-8425-36-2

Keyword(s): miRNA, Molecular dynamics, Thermodynamic integration.

Related Ontology Subjects/Areas/Topics: Agents ; Artificial Intelligence ; Bioinformatics ; Biomedical Engineering ; Enterprise Information Systems ; Information Systems Analysis and Specification ; Methodologies and Technologies ; Operational Research ; Simulation ; Structural Bioinformatics ; Structure Prediction

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.

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Paper citation in several formats:
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

@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},
}

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

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