2016
DOI: 10.1021/acs.jctc.6b00028
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Monte Carlo Tightly Bound Ion Model: Predicting Ion-Binding Properties of RNA with Ion Correlations and Fluctuations

Abstract: Experiments have suggested that ion correlation and fluctuation effects can be potentially important for multivalent ions in RNA folding. However, most existing computational methods for the ion electrostatics in RNA folding tend to ignore these effects. The previously reported Tightly Bound Ion (TBI) model can treat ion correlation and fluctuation but its applicability to biologically important RNAs is severely limited by the low computational efficiency. Here, based on Monte Carlo sampling for the many-body … Show more

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Cited by 40 publications
(71 citation statements)
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“…The TB region for a given RNA structure and ionic condition is usually a nonuniform thin layer surrounding the RNA surface. The rigorous demarcation of the TB and the DB regions can be found in previous publications (Tan and Chen 2005;He and Chen 2012;Sun and Chen 2016). In the MCTBI model, the TB ions and DB ions are treated as discrete particles (with the correlation effect) and continuum background (without the correlation effect), respectively.…”
Section: Methodsmentioning
confidence: 99%
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“…The TB region for a given RNA structure and ionic condition is usually a nonuniform thin layer surrounding the RNA surface. The rigorous demarcation of the TB and the DB regions can be found in previous publications (Tan and Chen 2005;He and Chen 2012;Sun and Chen 2016). In the MCTBI model, the TB ions and DB ions are treated as discrete particles (with the correlation effect) and continuum background (without the correlation effect), respectively.…”
Section: Methodsmentioning
confidence: 99%
“…Below we briefly summarize the main points of the model. Further details can be found in Sun and Chen (2016).…”
Section: Methodsmentioning
confidence: 99%
See 3 more Smart Citations