ArticleRNA (New York, N.Y.)2012
Improved prediction of RNA tertiary structure with insights into native state dynamics.
Article in RNA (New York, N.Y.), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
18 citing papers in PubMed.
- MiSiPi.Rna: an integrated tool for characterizing small regulatory RNA processing.RNA (New York, N.Y.) · 2026Article
- Allelic Variation at tRNA Genes in Three Nematode Species Indicates Mutation Load Despite Strong Purifying Selection.Genome biology and evolution · 2026Article
- LncPlankton: a comprehensive database of candidate lncRNAs from marine microbial eukaryotes.NAR genomics and bioinformatics · 2025Article
- cgRNASP: coarse-grained statistical potentials with residue separation for RNA structure evaluation.NAR genomics and bioinformatics · 2023Article
- Post-vaccine epidemiology of serotype 3 pneumococci identifies transformation inhibition through prophage-driven alteration of a non-coding RNA.Genome medicine · 2022Article
- 3dDNA: A Computational Method of Building DNA 3D Structures.Molecules (Basel, Switzerland) · 2022Article
- Computational Pipeline for Reference-Free Comparative Analysis of RNA 3D Structures Applied to SARS-CoV-2 UTR Models.International journal of molecular sciences · 2022Article
- Topological constraints of RNA pseudoknotted and loop-kissing motifs: applications to three-dimensional structure prediction.Nucleic acids research · 2020Article
- Advances in RNA 3D Structure Modeling Using Experimental Data.Frontiers in genetics · 2020Review
- Predicting 3D structure and stability of RNA pseudoknots in monovalent and divalent ion solutions.PLoS computational biology · 2018Article
- Hierarchical Assembly of RNA Three-Dimensional Structures Based on Loop Templates.The journal of physical chemistry. B · 2018Article
- A nucleobase-centered coarse-grained representation for structure prediction of RNA motifs.Nucleic acids research · 2018Article
- Capturing RNA Folding Free Energy with Coarse-Grained Molecular Dynamics Simulations.Scientific reports · 2017Article
- Structure Prediction: New Insights into Decrypting Long Noncoding RNAs.International journal of molecular sciences · 2016Review
- Predicting 3D Structure, Flexibility, and Stability of RNA Hairpins in Monovalent and Divalent Ion Solutions.Biophysical journal · 2015Article
- Coarse grained models reveal essential contributions of topological constraints to the conformational free energy of RNA bulges.The journal of physical chemistry. B · 2014Article
- The impact of a ligand binding on strand migration in the SAM-I riboswitch.PLoS computational biology · 2013Article
- Coarse-grained prediction of RNA loop structures.PloS one · 2012Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
The importance of RNA tertiary structure is evident from the growing number of published high resolution NMR and X-ray crystallographic structures of RNA molecules. These structures provide insights into function and create a knowledge base that is leveraged by programs such as Assemble, ModeRNA, RNABuilder, NAST, FARNA, Mc-Sym, RNA2D3D, and iFoldRNA for tertiary structure prediction and design. While these methods sample native-like RNA structures during simulations, all struggle to capture the native RNA conformation after scoring. We propose RSIM, an improved RNA fragment assembly method that preserves RNA global secondary structure while sampling conformations. This approach enhances the quality of predicted RNA tertiary structure, provides insights into the native state dynamics, and generates a powerful visualization of the RNA conformational space. RSIM is available for download from http://www.github.com/jpbida/rsim.
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Registered trials
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.