ArticleJournal of the American Chemical Society2008
Structural insight into RNA hairpin folding intermediates.
Article in Journal of the American Chemical Society, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
What it found
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Who cites it
37 citing papers in PubMed.
- Interpretation of Short RNA Thermal Unfolding Data Obtained by Circular Dichroism Using ChiraKit.Methods in molecular biology (Clifton, N.J.) · 2026Article
- A Review of Topological Data Analysis and Topological Deep Learning in Molecular Sciences.Journal of chemical information and modeling · 2025Review
- RNA Folding Based on 5 Beads Model and Multiscale Simulation.Interdisciplinary sciences, computational life sciences · 2023Article
- Folding@home: Achievements from over 20 years of citizen science herald the exascale era.Biophysical journal · 2023Review
- Folding@home: achievements from over twenty years of citizen science herald the exascale era.ArXiv · 2023Article
- Accelerating the Ensemble Convergence of RNA Hairpin Simulations with a Replica Exchange Structure Reservoir.Journal of chemical theory and computation · 2022Article
- Topological data analysis in biomedicine: A review.Journal of biomedical informatics · 2022Review
- Fluorescence-Based Binding Characterization of Small Molecule Ligands Targeting CUG RNA Repeats.International journal of molecular sciences · 2022Article
- Monovalent ions modulate the flux through multiple folding pathways of an RNA pseudoknot.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- IsRNA: An Iterative Simulated Reference State Approach to Modeling Correlated Interactions in RNA Folding.Journal of chemical theory and computation · 2018Article
- Conformational dynamics of the frameshift stimulatory structure in HIV-1.RNA (New York, N.Y.) · 2017Article
- Theory and Modeling of RNA Structure and Interactions with Metal Ions and Small Molecules.Annual review of biophysics · 2017Review
- Predicting the Kinetics of RNA Oligonucleotides Using Markov State Models.Journal of chemical theory and computation · 2017Article
- Free-energy landscape of a hyperstable RNA tetraloop.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Understanding the kinetic mechanism of RNA single base pair formation.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- De novo design of heat-repressible RNA thermosensors in E. coli.Nucleic acids research · 2015Article
- Article
- High-resolution reversible folding of hyperstable RNA tetraloops using molecular dynamics simulations.Proceedings of the National Academy of Sciences of the United States of America · 2013Review
- Mechanism of the hairpin folding transformation of thymine-cytosine-rich oligonucleotides induced by Hg(II) and Ag(I) ions.The European physical journal. E, Soft matter · 2013Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
Hairpins are a ubiquitous secondary structure motif in RNA molecules. Despite their simple structure, there is some debate over whether they fold in a two-state or multi-state manner. We have studied the folding of a small tetraloop hairpin using a serial version of replica exchange molecular dynamics on a distributed computing environment. On the basis of these simulations, we have identified a number of intermediates that are consistent with experimental results. We also find that folding is not simply the reverse of high-temperature unfolding and suggest that this may be a general feature of biomolecular folding.
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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.