ArticleJournal of structural biology2020
Inverse folding with RNA-As-Graphs produces a large pool of candidate sequences with target topologies.
Article in Journal of structural biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- VARIANT: Web Server for Decoding and Analyzing Viral Mutations at Genome and Protein Levels.Biophysical journal · 2026Article
- Open questions on viral frameshifting: Exploiting the structural plasticity of the frameshifting element for therapeutic intervention.Biophysical journal · 2026Review
- Computational approaches for RNA structure prediction and design.Cell reports. Physical science · 2026Article
- How large is the universe of RNA-like motifs? A clustering analysis of RNA graph motifs using topological descriptors.PLoS computational biology · 2025Article
- Conformational Analysis and Structure-Altering Mutations of the HIV-1 Frameshifting Element.International journal of molecular sciences · 2025Article
- A Cascade of Conformational Switches in SARS-CoV-2 Frameshifting: Coregulation by Upstream and Downstream Elements.Biochemistry · 2025Article
- Phase Space Invaders' podcast episode with Tamar Schlick: a trajectory from mathematics to biology.Biophysical reviews · 2025Article
- Heterogeneous and multiple conformational transition pathways between pseudoknots of the SARS-CoV-2 frameshift element.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Abolished frameshifting for predicted structure-stabilizing SARS-CoV-2 mutants: implications to alternative conformations and their statistical structural analyses.RNA (New York, N.Y.) · 2024Article
- An intricate balancing act: Upstream and downstream frameshift co-regulatory elements.bioRxiv : the preprint server for biology · 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
- 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
- To Knot or Not to Knot: Multiple Conformations of the SARS-CoV-2 Frameshifting RNA Element.Journal of the American Chemical Society · 2021Article
- To knot or not to knot: Multiple conformations of the SARS-CoV-2 frameshifting RNA element.bioRxiv : the preprint server for biology · 2021Article
- Finding recurrent RNA structural networks with fast maximal common subgraphs of edge-colored graphs.PLoS computational biology · 2021Article
- Structure-altering mutations of the SARS-CoV-2 frameshifting RNA element.Biophysical journal · 2021Article
- Graph, pseudoknot, and SARS-CoV-2 genomic RNA: A biophysical synthesis.Biophysical journal · 2021Article
- A Fiedler Vector Scoring Approach for Novel RNA Motif Selection.The journal of physical chemistry. B · 2021Article
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3 authors.
Funding
Abstract
We present an RNA-As-Graphs (RAG) based inverse folding algorithm, RAG-IF, to design novel RNA sequences that fold onto target tree graph topologies. The algorithm can be used to enhance our recently reported computational design pipeline (Jain et al., NAR 2018). The RAG approach represents RNA secondary structures as tree and dual graphs, where RNA loops and helices are coarse-grained as vertices and edges, opening the usage of graph theory methods to study, predict, and design RNA structures. Our recently developed computational pipeline for design utilizes graph partitioning (RAG-3D) and atomic fragment assembly (F-RAG) to design sequences to fold onto RNA-like tree graph topologies; the atomic fragments are taken from existing RNA structures that correspond to tree subgraphs. Because F-RAG may not produce the target folds for all designs, automated mutations by RAG-IF algorithm enhance the candidate pool markedly. The crucial residues for mutation are identified by differences between the predicted and the target topology. A genetic algorithm then mutates the selected residues, and the successful sequences are optimized to retain only the minimal or essential mutations. Here we evaluate RAG-IF for 6 RNA-like topologies and generate a large pool of successful candidate sequences with a variety of minimal mutations. We find that RAG-IF adds robustness and efficiency to our RNA design pipeline, making inverse folding motivated by graph topology rather than secondary structure more productive.
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