ArticleMethods in enzymology2019
Using Rosetta for RNA homology modeling.
Article in Methods in enzymology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Fast activity prediction of chemically modified siRNAs via structure-based energy calculations and inference-augmented tabular deep learning.Molecular therapy. Nucleic acids · 2026Article
- Crystal structures of type T archaeal ribonuclease P Rpp30, Rpp30/Pop5, and L7Ae provide insights into a reduced RNase P.Nucleic acids research · 2026Article
- Comprehensive analysis of Saccharomyces cerevisiae intron structures in vivo.Nature structural & molecular biology · 2025Article
- AI-Driven Deep Learning Techniques in Protein Structure Prediction.International journal of molecular sciences · 2024Review
- Article
- Assessment of three-dimensional RNA structure prediction in CASP15.bioRxiv : the preprint server for biology · 2023Article
- RNA 3D Modeling with FARFAR2, Online.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Recent advances in RNA structurome.Science China. Life sciences · 2022Review
- Structures of artificially designed discrete RNA nanoarchitectures at near-atomic resolution.Science advances · 2021Article
- Recent trends in biocatalysis.Chemical Society reviews · 2021Review
- De novo 3D models of SARS-CoV-2 RNA elements from consensus experimental secondary structures.Nucleic acids research · 2021Article
- FARFAR2: Improved De Novo Rosetta Prediction of Complex Global RNA Folds.Structure (London, England : 1993) · 2020Article
- A novel riboswitch classification based on imbalanced sequences achieved by machine learning.PLoS computational biology · 2020Article
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3 authors.
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Abstract
The three-dimensional structures of RNA molecules provide rich and often critical information for understanding their functions, including how they recognize small molecule and protein partners. Computational modeling of RNA 3D structure is becoming increasingly accurate, particularly with the availability of growing numbers of template structures already solved experimentally and the development of sequence alignment and 3D modeling tools to take advantage of this database. For several recent "RNA puzzle" blind modeling challenges, we have successfully identified useful template structures and achieved accurate structure predictions through homology modeling tools developed in the Rosetta software suite. We describe our semi-automated methodology here and walk through two illustrative examples: an adenine riboswitch aptamer, modeled from a template guanine riboswitch structure, and a SAM I/IV riboswitch aptamer, modeled from a template SAM I riboswitch structure.
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