A nucleobase-centered coarse-grained representation for structure prediction of RNA motifs

Poblete, Simon; Bottaro, Sandro; Bussi, Giovanni


We introduce the SPlit-and-conQueR (SPQR) model, a coarse-grained (CG) representation of RNA designed for structure prediction and refinement. In our approach, the representation of a nucleotide consists of a point particle for the phosphate group and an anisotropic particle for the nucleoside. The interactions are, in principle, knowledge-based potentials inspired by the ESCORE function, a basecentered scoring function. However, a special treatment is given to base-pairing interactions and certain geometrical conformations which are lost in a raw knowledge-based model. This results in a representation able to describe planar canonical and noncanonical base pairs and base-phosphate interactions and to distinguish sugar puckers and glycosidic torsion conformations. The model is applied to the folding of several structures, including duplexes with internal loops of non-canonical base pairs, tetraloops, junctions and a pseudoknot. For the majority of these systems, experimental structures are correctly predicted at the level of individual contacts. We also propose a method for efficiently reintroducing atomistic detail from the CG representation.

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Título según WOS: ID WOS:000426293300016 Not found in local WOS DB
Título de la Revista: NUCLEIC ACIDS RESEARCH
Volumen: 46
Número: 4
Fecha de publicación: 2018
Página de inicio: 1674
Página final: 1683


Notas: ISI