Nucleic acids modeling strategies

In another approach, He et al. (He et al., 2013) proposed a 2-site per nucleotide (NARES-2P, nucleic acid united residue 2-point model) CG model where chain connectivity, excluded volume and base dipole interactions are sufficient to form helical DNA and RNA structures. This model was parametrized using a bottom-up strategy by employing a set of statistical potentials, derived from DNA and RNA structures from the Protein Data Bank, and the Boltzmann inversion method to reproduce the structural features. The base-base interactions were parametrized by fitting the potential of mean force to detailed all-atoms MD simulations using also the Boltzmann inversion approach. The respective potentials do not explicitly define the nucleic-acid structure, dynamics and thermod3mamics, but are derived as potentials of mean force. By detailed analysis of the different contribution to the Hamiltonian, the authors determined that the multipole-multipole interactions are the principal factor responsible for the formation of regular structures, such as the double helical structures. 

We begin by discussing the modeling strategies which have been developed specifically to study nucleic acid... 

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