ArticleMethods in molecular biology (Clifton, N.J.)2016
A Method to Predict the Structure and Stability of RNA/RNA Complexes.
Article in Methods in molecular biology (Clifton, N.J.), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Enhancing RNA 3D Structure Prediction in CASP16: Integrating Physics-Based Modeling With Machine Learning for Improved Predictions.Proteins · 2026Article
- RNA-Puzzles Round V: blind predictions of 23 RNA structures.Nature methods · 2025Article
- Machine learning in RNA structure prediction: Advances and challenges.Biophysical journal · 2024Review
- Advancing RNA 3D structure prediction: Exploring hierarchical and hybrid approaches in CASP15.Proteins · 2023Article
- RNet: a network strategy to predict RNA binding preferences.Briefings in bioinformatics · 2023Article
- Article
- An NMR-based approach reveals the core structure of the functional domain of SINEUP lncRNAs.Nucleic acids research · 2020Article
- HNADOCK: a nucleic acid docking server for modeling RNA/DNA-RNA/DNA 3D complex structures.Nucleic acids research · 2019Article
- Determination of an effective scoring function for RNA-RNA interactions with a physics-based double-iterative method.Nucleic acids research · 2018Article
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Authors and funding
2 authors.
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Abstract
RNA/RNA interactions are essential for genomic RNA dimerization and regulation of gene expression. Intermolecular loop-loop base pairing is a widespread and functionally important tertiary structure motif in RNA machinery. However, computational prediction of intermolecular loop-loop base pairing is challenged by the entropy and free energy calculation due to the conformational constraint and the intermolecular interactions. In this chapter, we describe a recently developed statistical mechanics-based method for the prediction of RNA/RNA complex structures and stabilities. The method is based on the virtual bond RNA folding model (Vfold). The main emphasis in the method is placed on the evaluation of the entropy and free energy for the loops, especially tertiary kissing loops. The method also uses recursive partition function calculations and two-step screening algorithm for large, complicated structures of RNA/RNA complexes. As case studies, we use the HIV-1 Mal dimer and the siRNA/HIV-1 mutant (T4) to illustrate the method.
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