ReviewJournal of physics. Condensed matter : an Institute of Physics journal2010
Computational approaches to 3D modeling of RNA.
Review in Journal of physics. Condensed matter : an Institute of Physics journal, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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
63 citing papers in PubMed.
- Article
- Structural Prediction of Coronavirus s2m Kissing Complexes and Extended Duplexes.ACS physical chemistry Au · 2025Article
- Comparative analysis of predicted DNA secondary structures infers complex human centromere topology.American journal of human genetics · 2024Article
- lociPARSE: A Locality-aware Invariant Point Attention Model for Scoring RNA 3D Structures.Journal of chemical information and modeling · 2024Article
- lociPARSE: a locality-aware invariant point attention model for scoring RNA 3D structures.bioRxiv : the preprint server for biology · 2024Article
- RNA 3D Structure Prediction: Progress and Perspective.Molecules (Basel, Switzerland) · 2023Review
- Nucleic acid nanostructures forApplied physics reviews · 2023Review
- FebRNA: An automated fragment-ensemble-based model for building RNA 3D structures.Biophysical journal · 2022Article
- RNAloops: a database of RNA multiloops.Bioinformatics (Oxford, England) · 2022Article
- "Bind, cleave and leave": multiple turnover catalysis of RNA cleavage by bulge-loop inducing supramolecular conjugates.Nucleic acids research · 2022Article
- Modeling Noncanonical RNA Base Pairs by a Coarse-Grained IsRNA2 Model.The journal of physical chemistry. B · 2021Article
- IsRNA1:Journal of chemical theory and computation · 2021Article
- A Fiedler Vector Scoring Approach for Novel RNA Motif Selection.The journal of physical chemistry. B · 2021Article
- SHAPER: A Web Server for Fast and Accurate SHAPE Reactivity Prediction.Frontiers in molecular biosciences · 2021Article
- FARFAR2: Improved De Novo Rosetta Prediction of Complex Global RNA Folds.Structure (London, England : 1993) · 2020Article
- ENTRNA: a framework to predict RNA foldability.BMC bioinformatics · 2019Article
- Adventures with RNA graphs.Methods (San Diego, Calif.) · 2018Review
- Quantitative Understanding of SHAPE Mechanism from RNA Structure and Dynamics Analysis.The journal of physical chemistry. B · 2018Article
- Molecular chaperones maximize the native state yield on biological times by driving substrates out of equilibrium.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- F-RAG: Generating Atomic Coordinates from RNA Graphs by Fragment Assembly.Journal of molecular biology · 2017Article
3 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
Many exciting discoveries have recently revealed the versatility of RNA and its importance in a variety of functions within the cell. Since the structural features of RNA are of major importance to their biological function, there is much interest in predicting RNA structure, either in free form or in interaction with various ligands, including proteins, metabolites and other molecules. In recent years, an increasing number of researchers have developed novel RNA algorithms for predicting RNA secondary and tertiary structures. In this review, we describe current experimental and computational advances and discuss recent ideas that are transforming the traditional view of RNA folding. To evaluate the performance of the most recent RNA 3D folding algorithms, we provide a comparative study in order to test the performance of available 3D structure prediction algorithms for an RNA data set of 43 structures of various lengths and motifs. We find that the algorithms vary widely in terms of prediction quality across different RNA lengths and topologies; most predictions have very large root mean square deviations from the experimental structure. We conclude by outlining some suggestions for future RNA folding research.
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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.