ArticleThe journal of physical chemistry letters2018
Molecular Dynamics Simulations Reveal an Interplay between SHAPE Reagent Binding and RNA Flexibility.
Article in The journal of physical chemistry letters, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
21 citing papers in PubMed.
- Markov models of SHAPE data improve secondary structure prediction.bioRxiv : the preprint server for biology · 2026Article
- Decoding the Structural Complexity of Viral RNAs with SHAPE to Guide Antiviral Therapeutics.Viruses · 2026Review
- DeepRMSF: a deep learning-based automated approach for predicting atomic-level flexibility in RNA structure.Briefings in bioinformatics · 2026Article
- Consistent features observed in structural probing data of eukaryotic RNAs.NAR genomics and bioinformatics · 2025Article
- IPANEMAP Suite: a pipeline for probing-informed RNA structure modeling.NAR genomics and bioinformatics · 2025Article
- SHAPE Probing to Screen Computationally Designed RNA.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Molecular Dynamics Simulations with Grand-Canonical Reweighting Suggest Cooperativity Effects in RNA Structure Probing Experiments.Journal of chemical theory and computation · 2023Article
- Recognizing the power of machine learning and other computational methods to accelerate progress in small molecule targeting of RNA.RNA (New York, N.Y.) · 2023Article
- RNA:RNA interaction in ternary complexes resolved by chemical probing.RNA (New York, N.Y.) · 2023Article
- Structural characterization of a new subclass of panicum mosaic virus-like 3' cap-independent translation enhancer.Nucleic acids research · 2022Article
- An overview of structural approaches to study therapeutic RNAs.Frontiers in molecular biosciences · 2022Review
- Insights into the secondary and tertiary structure of the Bovine Viral Diarrhea Virus Internal Ribosome Entry Site.RNA biology · 2022Article
- Progress toward SHAPE Constrained Computational Prediction of Tertiary Interactions in RNA Structure.Non-coding RNA · 2021Article
- Characteristic chemical probing patterns of loop motifs improve prediction accuracy of RNA secondary structures.Nucleic acids research · 2021Article
- Machine learning a model for RNA structure prediction.NAR genomics and bioinformatics · 2020Article
- IPANEMAP: integrative probing analysis of nucleic acids empowered by multiple accessibility profiles.Nucleic acids research · 2020Article
- Challenges and perspectives for structural biology of lncRNAs-the example of the Xist lncRNA A-repeats.Journal of molecular cell biology · 2019Article
- reactIDR: evaluation of the statistical reproducibility of high-throughput structural analyses towards a robust RNA structure prediction.BMC bioinformatics · 2019Article
- High-throughput determination of RNA structures.Nature reviews. Genetics · 2018Review
- An RNA-binding compound that stabilizes the HIV-1 gRNA packaging signal structure and specifically blocks HIV-1 RNA encapsidation.Retrovirology · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The function of RNA molecules usually depends on their overall fold and on the presence of specific structural motifs. Chemical probing methods are routinely used in combination with nearest-neighbor models to determine RNA secondary structure. Among the available methods, SHAPE is relevant due to its capability to probe all RNA nucleotides and the possibility to be used in vivo. However, the structural determinants for SHAPE reactivity and its mechanism of reaction are still unclear. Here molecular dynamics simulations and enhanced sampling techniques are used to predict the accessibility of nucleotide analogs and larger RNA structural motifs to SHAPE reagents. We show that local RNA reconformations are crucial in allowing reagents to reach the 2'-OH group of a particular nucleotide and that sugar pucker is a major structural factor influencing SHAPE reactivity.
Indexed as
Identifiers
What 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.