ArticleWSEAS transactions on mathematics2013
Network Theory Tools for RNA Modeling.
Article in WSEAS transactions on mathematics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 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
18 citing papers in PubMed.
- Prediction of pyrazinamide resistance inJAC-antimicrobial resistance · 2024Article
- RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers.RNA (New York, N.Y.) · 2020Article
- RNA-Puzzles toolkit: a computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools.Nucleic acids research · 2020Article
- An extended dual graph library and partitioning algorithm applicable to pseudoknotted RNA structures.Methods (San Diego, Calif.) · 2019Article
- A pipeline for computational design of novel RNA-like topologies.Nucleic acids research · 2018Article
- Dual Graph Partitioning Highlights a Small Group of Pseudoknot-Containing RNA Submotifs.Genes · 2018Article
- Adventures with RNA graphs.Methods (San Diego, Calif.) · 2018Review
- Opportunities and Challenges in RNA Structural Modeling and Design.Biophysical journal · 2017Article
- Using sequence signatures and kink-turn motifs in knowledge-based statistical potentials for RNA structure prediction.Nucleic acids research · 2017Article
- Capturing RNA Folding Free Energy with Coarse-Grained Molecular Dynamics Simulations.Scientific reports · 2017Article
- Partitioning and Classification of RNA Secondary Structures into Pseudonotted and Pseudoknot-free Regions Using a Graph-Theoretical Approach.IAENG international journal of computer science · 2017Article
- New insights from cluster analysis methods for RNA secondary structure prediction.Wiley interdisciplinary reviews. RNA · 2016Review
- Predicting Large RNA-Like Topologies by a Knowledge-Based Clustering Approach.Journal of molecular biology · 2016Article
- RAG-3D: a search tool for RNA 3D substructures.Nucleic acids research · 2015Article
- Graph-based sampling for approximating global helical topologies of RNA.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- RiboFSM: frequent subgraph mining for the discovery of RNA structures and interactions.BMC bioinformatics · 2014Article
- RNA graph partitioning for the discovery of RNA modularity: a novel application of graph partition algorithm to biology.PloS one · 2014Article
- Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
An introduction into the usage of graph or network theory tools for the study of RNA molecules is presented. By using vertices and edges to define RNA secondary structures as tree and dual graphs, we can enumerate, predict, and design RNA topologies. Graph connectivity and associated Laplacian eigenvalues relate to biological properties of RNA and help understand RNA motifs as well as build, by computational design, various RNA target structures. Importantly, graph theoretical representations of RNAs reduce drastically the conformational space size and therefore simplify modeling and prediction tasks. Ongoing challenges remain regarding general RNA design, representation of RNA pseudoknots, and tertiary structure prediction. Thus, developments in network theory may help advance RNA biology.
Indexed as
Identifiers
25414570PMC4235620What OpenQuestion holds
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.