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Chapitre D'ouvrage Année : 2005

Molecular Dynamics Simulations of RNA Systems

Résumé

As a result of important methodological advances, the number of molecular dynamics (MD) simulations related to RNA systems has become significant, and simulations on more than 30 different RNA, RNA–protein and RNA–ligand systems have been reported. However, the simulation of the dynamics of such systems presents specific problems associated with the complex three-dimensional folds adopted by their highly charged polyanionic backbone and by the large variety of naturally modified nucleotides they comprise. It is, thus, timely to present the current state of the art of MD simulations of RNA systems in a comprehensive and practically oriented manner. Several reviews on nucleic acid MD simulations already address important methodological issues. Here, we will focus on how to setup a MD simulation of an RNA system by using explicit representation of solvent and Ewald summation methods for the treatment of the long-range electrostatic interactions. Specific features related to MD simulations of RNA systems using implicit solvation models can be found. The simulation protocols that will be described in the following refer mainly to our own experience with the AMBER program with which we are most familiar and which is used in many laboratories working on nucleic acids. They should be easily transposable to other MD packages.
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Dates et versions

hal-03811673 , version 1 (16-11-2022)

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  • HAL Id : hal-03811673 , version 1

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Pascal Auffinger, Andrea C. Vaiana. Molecular Dynamics Simulations of RNA Systems. Handbook of RNA biochemistry, 2005. ⟨hal-03811673⟩

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