Journal
CHEMICAL PAPERS
Volume 77, Issue 5, Pages 2437-2445Publisher
SPRINGER INT PUBL AG
DOI: 10.1007/s11696-022-02634-x
Keywords
Nucleic acids; All-atom structure reconstruction; NARES-2P
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Nucleic acids are essential cellular components that have been studied using both experimental and theoretical approaches. Coarse-grain modeling, such as the NARES-2P model, allows for the study of nucleic acids on a longer time scale. This article presents a new software that reconstructs atomistic details from the NARES-2P model, which has been successfully applied to study various nucleic acid structures and behaviors.
Nucleic acids are one of the most important cellular components. These molecules have been studied both experimentally and theoretically. As all-atom simulations are still limited to short time scales, coarse-grain modeling allows to study of those molecules on a longer time scale. Nucleic-Acid united RESidue (NARES-2P) is a low-resolution coarse-grained model with two centers of interaction per repeating unit. It has been successfully applied to study DNA self-assembly and telomeric properties. This force field enables the study of nucleic acids Behavior on a long time scale but lacks atomistic details. In this article, we present new software to reconstruct atomistic details from the NARES-2P model. It has been applied to RNA pseudoknot, nucleic acid four-way junction, G-quadruplex and DNA duplex converted to NARES-2P model and back. Moreover, it was applied to DNA structure folded and self-assembled with NARES-2P.
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