A nucleobase-centered coarse-grained representation for structure prediction of RNA motifs
| Autor: | Poblete, Simón, Bottaro, Sandro, Bussi, Giovanni |
|---|---|
| Rok vydání: | 2017 |
| Předmět: | |
| Zdroj: | Nucleic Acids Res. 46, 1674 (2018) |
| Druh dokumentu: | Working Paper |
| DOI: | 10.1093/nar/gkx1269 |
| Popis: | We introduce the SPlit-and-conQueR (SPQR) model, a coarse-grained 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 base-centered scoring function. However, a special treatment is given to base-pairing interactions and certain geometrical conformations which are lost in a raw knowledge-base model. This results in a representation able to describe planar canonical and non-canonical 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 coarse-grained representation. Comment: Accepted for publication on Nucleic Acids Research |
| Databáze: | arXiv |
| Externí odkaz: |
|