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RNAJP: enhanced RNA 3D structure predictions with non-canonical interactions and global topology sampling
- Source :
- Nucleic Acids Research. 51:3341-3356
- Publication Year :
- 2023
- Publisher :
- Oxford University Press (OUP), 2023.
-
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.
- Subjects :
- Genetics
Subjects
Details
- ISSN :
- 13624962 and 03051048
- Volume :
- 51
- Database :
- OpenAIRE
- Journal :
- Nucleic Acids Research
- Accession number :
- edsair.doi...........9e17cf9a7834109bcbe6088c9921d483