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Improvement of RNA Simulations with Torsional Revisions of the AMBER Force Field

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Book cover Biomolecular Simulations

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2022))

Abstract

Our current knowledge on the unique roles of RNA in cells makes it vital to investigate the properties of RNA systems using computational methods because of the potential pharmaceutical applications. With the continuous advancement of computer technology, it is now possible to study RNA folding. Molecular mechanics calculations are useful in discovering the structural and thermodynamic properties of RNA systems. Yet, the predictions depend on the quality of the RNA force field, which is a set of parameters describing the potential energy of the system. Torsional parameters are one of the terms in a force field that can be revised using physics-based approaches. This chapter focuses on improvements provided by revisions of torsional parameters of the AMBER (Assisted Model Building with Energy Refinement) RNA force field. The theory behind torsional revisions and re-parameterization of several RNA torsions is briefly described. Applications of the revised torsional parameters to study RNA nucleosides, single-stranded RNA tetramers, and RNA repeat expansions are described in detail. It is concluded that RNA force fields require constant revisions and should be benchmarked against diverse RNA systems such as single strands and internal loops in order to test their qualities.

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Acknowledgments

I would like to thank the Department of Chemistry and Biochemistry, Florida Atlantic University, for financial support, and Prof. Douglas H. Turner for valuable suggestions while writing this book chapter.

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  1. Department of Chemistry and Biochemistry, Florida Atlantic University, Jupiter, FL, USA

    Ilyas Yildirim

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  1. Ilyas Yildirim
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Correspondence to Ilyas Yildirim .

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  1. Structural Bioinformatics Unit, Institut Pasteur, CNRS UMR 3528, Paris, France

    Massimiliano Bonomi

  2. Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy

    Carlo Camilloni

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Yildirim, I. (2019). Improvement of RNA Simulations with Torsional Revisions of the AMBER Force Field. In: Bonomi, M., Camilloni, C. (eds) Biomolecular Simulations. Methods in Molecular Biology, vol 2022. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9608-7_3

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