ArticleRNA (New York, N.Y.)2014
Predicting structure and stability for RNA complexes with intermolecular loop-loop base-pairing.
Article in RNA (New York, N.Y.), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 23 citations in OpenAlex.
- RNA-Puzzles Round V: blind predictions of 23 RNA structures.Nature methods · 2025Article
- cRNAsp12 Web Server for the Prediction of Circular RNA Secondary Structures and Stabilities.International journal of molecular sciences · 2023Article
- VfoldMCPX: predicting multistrand RNA complexes.RNA (New York, N.Y.) · 2022Article
- Landscape Zooming toward the Prediction of RNA Cotranscriptional Folding.Journal of chemical theory and computation · 2022Article
- Thermostability, Tunability, and Tenacity of RNA as Rubbery Anionic Polymeric Materials in Nanotechnology and Nanomedicine-Specific Cancer Targeting with Undetectable Toxicity.Chemical reviews · 2021Review
- Topological constraints of RNA pseudoknotted and loop-kissing motifs: applications to three-dimensional structure prediction.Nucleic acids research · 2020Article
- Structure folding of RNA kissing complexes in salt solutions: predicting 3D structure, stability, and folding pathway.RNA (New York, N.Y.) · 2019Article
- Editorial: Genome Invading RNA Networks.Frontiers in microbiology · 2018Article
- Theory and Modeling of RNA Structure and Interactions with Metal Ions and Small Molecules.Annual review of biophysics · 2017Review
- On the conformational stability of the smallest RNA kissing complexes maintained through two G·C base pairs.Biochemical and biophysical research communications · 2017Article
- Multistrand Structure Prediction of Nucleic Acid Assemblies and Design of RNA Switches.Nano letters · 2016Article
- A Method to Predict the Structure and Stability of RNA/RNA Complexes.Methods in molecular biology (Clifton, N.J.) · 2016Article
- Computational and experimental studies of reassociating RNA/DNA hybrids containing split functionalities.Methods in enzymology · 2015Article
- A Method to Predict the 3D Structure of an RNA Scaffold.Methods in molecular biology (Clifton, N.J.) · 2015Article
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- Physics-based RNA structure prediction.Biophysics reportsArticle
- Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
RNA loop-loop interactions are essential for genomic RNA dimerization and regulation of gene expression. In this article, a statistical mechanics-based computational method that predicts the structures and thermodynamic stabilities of RNA complexes with loop-loop kissing interactions is described. The method accounts for the entropy changes for the formation of loop-loop interactions, which is a notable advancement that other computational models have neglected. Benchmark tests with several experimentally validated systems show that the inclusion of the entropy parameters can indeed improve predictions for RNA complexes. Furthermore, the method can predict not only the native structures of RNA/RNA complexes but also alternative metastable structures. For instance, the model predicts that the SL1 domain of HIV-1 RNA can form two different dimer structures with similar stabilities. The prediction is consistent with experimental observation. In addition, the model predicts two different binding sites for hTR dimerization: One binding site has been experimentally proposed, and the other structure, which has a higher stability, is structurally feasible and needs further experimental validation.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.