ArticleJournal of molecular biology2022
Exploring the Energy Landscape of Riboswitches Using Collective Variables Based on Tertiary Contacts.
Article in Journal of molecular biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
What it found
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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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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.
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Who cites it
8 citing papers in PubMed, 8 citations in OpenAlex.
- Article
- Structural basis for Mg²⁺-glycine synergy in the tandem glycine riboswitch revealed by cryo-EM.Npj structural biology · 2026Article
- Cryo-EM reveals remodeling of a tandem riboswitch at 2.9 Å resolution.Research square · 2025Article
- Supercomputing in the biological sciences: Toward Zettascale and Yottascale simulations.Current opinion in structural biology · 2024Review
- Embracing exascale computing in nucleic acid simulations.Current opinion in structural biology · 2024Review
- Article
- Biophysical and Integrative Characterization of Protein Intrinsic Disorder as a Prime Target for Drug Discovery.Biomolecules · 2023Review
- Regulatory Mechanisms through RNA Conformational Switching and Dynamics.Journal of molecular biology · 2022Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
Messenger RNA regulatory elements, such as riboswitches, can display a high degree of flexibility. By characterizing their energy landscapes, and corresponding distributions of 3D configurations, structure-function relationships can be elucidated. Molecular dynamics simulation with enhanced sampling is an important strategy used to computationally access free energy landscapes characterizing the accessible 3D conformations of RNAs. While tertiary contacts are thought to play important roles in RNA dynamics, it is difficult, in explicit solvent, to sample the formation and breakage of tertiary contacts, such as helix-helix interactions, pseudoknot interactions, and junction interactions, while maintaining intact secondary structure elements. To this end, we extend previously developed collective variables and metadynamics efforts, to establish a simple metadynamics protocol, which utilizes only one collective variable, based on multiple tertiary contacts, to characterize the underlying free energy landscape of any RNA molecule. We develop a modified collective variable, the tertiary contacts distance (Q
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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.