ArticleNucleic acids research2018
A pipeline for computational design of novel RNA-like topologies.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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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.
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Who cites it
19 citing papers in PubMed.
- Phase Space Invaders' podcast episode with Tamar Schlick: a trajectory from mathematics to biology.Biophysical reviews · 2025Article
- RNA fold prediction by Monte Carlo in graph space and the statistical mechanics of tertiary interactions.RNA (New York, N.Y.) · 2024Article
- Evolution of coronavirus frameshifting elements: Competing stem networks explain conservation and variability.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- FebRNA: An automated fragment-ensemble-based model for building RNA 3D structures.Biophysical journal · 2022Article
- RNA-As-Graphs Motif Atlas-Dual Graph Library of RNA Modules and Viral Frameshifting-Element Applications.International journal of molecular sciences · 2022Article
- Length-dependent motions of SARS-CoV-2 frameshifting RNA pseudoknot and alternative conformations suggest avenues for frameshifting suppression.Nature communications · 2022Article
- Length-dependent motions of SARS-CoV-2 frameshifting RNA pseudoknot and alternative conformations suggest avenues for frameshifting suppression.Research square · 2022Article
- RiboDraw: semiautomated two-dimensional drawing of RNA tertiary structure diagrams.NAR genomics and bioinformatics · 2021Article
- Biomolecular Modeling and Simulation: A Prospering Multidisciplinary Field.Annual review of biophysics · 2021Article
- Structure-altering mutations of the SARS-CoV-2 frameshifting RNA element.Biophysical journal · 2021Article
- A Fiedler Vector Scoring Approach for Novel RNA Motif Selection.The journal of physical chemistry. B · 2021Article
- Structure-Altering Mutations of the SARS-CoV-2 Frame Shifting RNA Element.bioRxiv : the preprint server for biology · 2020Article
- Identification of novel RNA design candidates by clustering the extended RNA-As-Graphs library.Biochimica et biophysica acta. General subjects · 2020Article
- Inverse folding with RNA-As-Graphs produces a large pool of candidate sequences with target topologies.Journal of structural biology · 2020Article
- RAG-Web: RNA structure prediction/design using RNA-As-Graphs.Bioinformatics (Oxford, England) · 2020Article
- Zinc-finger protein CNBP alters the 3-D structure of lncRNA Braveheart in solution.Nature communications · 2020Article
- An extended dual graph library and partitioning algorithm applicable to pseudoknotted RNA structures.Methods (San Diego, Calif.) · 2019Article
- Dual Graph Partitioning Highlights a Small Group of Pseudoknot-Containing RNA Submotifs.Genes · 2018Article
- Adventures with RNA graphs.Methods (San Diego, Calif.) · 2018Review
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Authors and funding
4 authors.
Funding
Abstract
Designing novel RNA topologies is a challenge, with important therapeutic and industrial applications. We describe a computational pipeline for design of novel RNA topologies based on our coarse-grained RNA-As-Graphs (RAG) framework. RAG represents RNA structures as tree graphs and describes RNA secondary (2D) structure topologies (currently up to 13 vertices, ≈260 nucleotides). We have previously identified novel graph topologies that are RNA-like among these. Here we describe a systematic design pipeline and illustrate design for six broad design problems using recently developed tools for graph-partitioning and fragment assembly (F-RAG). Following partitioning of the target graph, corresponding atomic fragments from our RAG-3D database are combined using F-RAG, and the candidate atomic models are scored using a knowledge-based potential developed for 3D structure prediction. The sequences of the top scoring models are screened further using available tools for 2D structure prediction. The results indicate that our modular approach based on RNA-like topologies rather than specific 2D structures allows for greater flexibility in the design process, and generates a large number of candidate sequences quickly. Experimental structure probing using SHAPE-MaP for two sequences agree with our predictions and suggest that our combined tools yield excellent candidates for further sequence and experimental screening.
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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.