期刊
NUCLEIC ACIDS RESEARCH
卷 46, 期 4, 页码 1674-1683出版社
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkx1269
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资金
- European Research Council under the European Union
- ERC [306662]
- S-RNA-S
- Scuola Internazionale Superiore di Studi Avanzati (SISSA)
- European Research Council (ERC) [306662] Funding Source: European Research Council (ERC)
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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