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J Chem Phys. 2017 Jan 21;146(3):035101. doi: 10.1063/1.4972986.

Fast coarse-grained model for RNA titration.

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Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ave. do café, s/no, BR-14040-903 Ribeirão Preto, São Paulo, Brazil.
Laboratoire de Biochimie Theórique, UPR 9080 CNRS, Institut de Biologie Physico Chimique, Université Paris Diderot - Paris 7 et Université Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France.


A new numerical scheme for RNA (ribonucleic acid) titration based on the Debye-Hückel framework for the salt description is proposed in an effort to reduce the computational costs for further applications to study protein-RNA systems. By means of different sets of Monte Carlo simulations, we demonstrated that this new scheme is able to correctly reproduce the experimental titration behavior and salt pKa shifts. In comparison with other theoretical approaches, similar or even better outcomes are achieved at much lower computational costs. The model was tested on the lead-dependent ribozyme, the branch-point helix, and the domain 5 from Azotobacter vinelandii Intron 5.

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