ArticleJournal of chemical theory and computation2012
Predicting ion-nucleic acid interactions by energy landscape-guided sampling.
Article in Journal of chemical theory and computation, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 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.
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.
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Who cites it
14 citing papers in PubMed, 21 citations in OpenAlex.
- Driving forces of RNA condensation revealed through coarse-grained modeling with explicit MgProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Landscape Zooming toward the Prediction of RNA Cotranscriptional Folding.Journal of chemical theory and computation · 2022Article
- Predicting Monovalent Ion Correlation Effects in Nucleic Acids.ACS omega · 2019Article
- Predicting Ion Effects in an RNA Conformational Equilibrium.The journal of physical chemistry. B · 2017Article
- MCTBI: a web server for predicting metal ion effects in RNA structures.RNA (New York, N.Y.) · 2017Article
- Theory Meets Experiment: Metal Ion Effects in HCV Genomic RNA Kissing Complex Formation.Frontiers in molecular biosciences · 2017Review
- A New Method to Predict Ion Effects in RNA Folding.Methods in molecular biology (Clifton, N.J.) · 2017Article
- Monte Carlo Tightly Bound Ion Model: Predicting Ion-Binding Properties of RNA with Ion Correlations and Fluctuations.Journal of chemical theory and computation · 2016Article
- Generalized Manning Condensation Model Captures the RNA Ion Atmosphere.Physical review letters · 2015Article
- Features of CPB: a Poisson-Boltzmann solver that uses an adaptive Cartesian grid.Journal of computational chemistry · 2015Article
- Article
- Many-body effect in ion binding to RNA.The Journal of chemical physics · 2014Article
- Exploring the electrostatic energy landscape for tetraloop-receptor docking.Physical chemistry chemical physics : PCCP · 2014Article
- Reduced model captures Mg(2+)-RNA interaction free energy of riboswitches.Biophysical journal · 2014Article
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 at 1 institution in 1 country.
Funding
Abstract
The recently developed Tightly Bound Ion (TBI) model offers improved predictions for ion effect in nucleic acid systems by accounting for ion correlation and fluctuation effects. However, further application of the model to larger systems is limited by the low computational efficiency of the model. Here, we develop a new computational efficient TBI model using free energy landscape-guided sampling method. The method leads to drastic reduction in the computer time by a factor of 50 for RNAs of 50-100 nucleotides long. The improvement in the computational efficiency would be more significant for larger structures. To test the new method, we apply the model to predict the free energies and the number of bound ions for a series of RNA folding systems. The validity of this new model is supported by the nearly exact agreement with the results from the original TBI model and the agreement with the experimental data. The method may pave the way for further applications of the TBI model to treat a broad range of biologically significant systems such as tetraloop-receptor and riboswitches.
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.