ArticleRNA (New York, N.Y.)2020
Hierarchical natural move Monte Carlo refines flexible RNA structures into cryo-EM densities.
Article in RNA (New York, N.Y.), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed, 8 citations in OpenAlex.
- The cryo-EM structure of bacteriophage PRR1 and its role in conjugation inhibition.Journal of virology · 2026Article
- Suppressing Transfer of Antibiotic Resistance by a Small RNA Virus.bioRxiv : the preprint server for biology · 2026Article
- Removal ofScience (New York, N.Y.) · 2024Article
- Structural basis of Acinetobacter type IV pili targeting by an RNA virus.Nature communications · 2024Article
- Review
- Article
- Transcriptional Riboswitches Integrate Timescales for Bacterial Gene Expression Control.Frontiers in molecular biosciences · 2020Review
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Authors and funding
6 authors at 3 institutions in 2 countries.
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Abstract
Ribonucleic acids (RNAs) play essential roles in living cells. Many of them fold into defined three-dimensional (3D) structures to perform functions. Recent advances in single-particle cryo-electron microscopy (cryo-EM) have enabled structure determinations of RNA to atomic resolutions. However, most RNA molecules are structurally flexible, limiting the resolution of their structures solved by cryo-EM. In modeling these molecules, several computational methods are limited by the requirement of massive computational resources and/or the low efficiency in exploring large-scale structural variations. Here we use hierarchical natural move Monte Carlo (HNMMC), which takes advantage of collective motions for groups of nucleic acid residues, to refine RNA structures into their cryo-EM maps, preserving atomic details in the models. After validating the method on a simulated density map of tRNA, we applied it to objectively obtain the model of the folding intermediate for the specificity domain of ribonuclease P from
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