RNAJP: enhanced RNA 3D structure predictions with non-canonical interactions and global topology sampling.
Nucleic Acids Res
; 51(7): 3341-3356, 2023 04 24.
Article
em En
| MEDLINE
| ID: mdl-36864729
ABSTRACT
RNA 3D structures are critical for understanding their functions. However, only a limited number of RNA structures have been experimentally solved, so computational prediction methods are highly desirable. Nevertheless, accurate prediction of RNA 3D structures, especially those containing multiway junctions, remains a significant challenge, mainly due to the complicated non-canonical base pairing and stacking interactions in the junction loops and the possible long-range interactions between loop structures. Here we present RNAJP ('RNA Junction Prediction'), a nucleotide- and helix-level coarse-grained model for the prediction of RNA 3D structures, particularly junction structures, from a given 2D structure. Through global sampling of the 3D arrangements of the helices in junctions using molecular dynamics simulations and in explicit consideration of non-canonical base pairing and base stacking interactions as well as long-range loop-loop interactions, the model can provide significantly improved predictions for multibranched junction structures than existing methods. Moreover, integrated with additional restraints from experiments, such as junction topology and long-range interactions, the model may serve as a useful structure generator for various applications.
Texto completo:
1
Base de dados:
MEDLINE
Assunto principal:
RNA
/
Simulação de Dinâmica Molecular
Tipo de estudo:
Prognostic_studies
/
Risk_factors_studies
Idioma:
En
Ano de publicação:
2023
Tipo de documento:
Article