ArticleThe Journal of chemical physics2010
Computing the conformational entropy for RNA folds.
Article in The Journal of chemical physics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Structural and Thermodynamic Properties of RNA Molecules Using a Knowledge-Based Model.Journal of chemical theory and computation · 2026Article
- 3dRNA: Building RNA 3D structure with improved template library.Computational and structural biotechnology journal · 2020Article
- Topological Constraints and Their Conformational Entropic Penalties on RNA Folds.Biophysical journal · 2018Article
- Theory and Modeling of RNA Structure and Interactions with Metal Ions and Small Molecules.Annual review of biophysics · 2017Review
- RPI-Bind: a structure-based method for accurate identification of RNA-protein binding sites.Scientific reports · 2017Article
- Structure Prediction of RNA Loops with a Probabilistic Approach.PLoS computational biology · 2016Article
- RPI-Pred: predicting ncRNA-protein interaction using sequence and structural information.Nucleic acids research · 2015Article
- Article
- Conformational entropy of the RNA phosphate backbone and its contribution to the folding free energy.Biophysical journal · 2014Article
- Tertiary structure-based analysis of microRNA-target interactions.RNA (New York, N.Y.) · 2013Article
- Free energy cost of stretching mRNA hairpin loops inhibits small RNA binding.Biophysical journal · 2013Article
- Characterising RNA secondary structure space using information entropy.BMC bioinformatics · 2013Article
- Coarse-grained prediction of RNA loop structures.PloS one · 2012Article
- Structure and stability of RNA/RNA kissing complex: with application to HIV dimerization initiation signal.RNA (New York, N.Y.) · 2011Article
- Physics-based de novo prediction of RNA 3D structures.The journal of physical chemistry. B · 2011Article
- Modeling loop entropy.Methods in enzymology · 2011Review
- Assembly and activation of a kinase ribozyme.RNA (New York, N.Y.) · 2010Article
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2 authors.
Funding
Abstract
We develop a polymer physics-based method to compute the conformational entropy for RNA tertiary folds, namely, conformations consisting of multiple helices connected through (cross-linked) loops. The theory is based on a virtual bond conformational model for the nucleotide chain. A key issue in the calculation of the entropy is how to treat the excluded volume interactions. The weak excluded volume interference between the different loops leads to the decomposition of the whole structure into a number of three-body building blocks, each consisting of a loop and two helices connected to the two ends of the loop. The simple construct of the three-body system allows an accurate computation for the conformational entropy for each building block. The assembly of the building blocks gives the entropy of the whole structure. This approach enables treatment of molten globule-like folds (partially unfolded tertiary structures) for RNAs. Extensive tests against experiments and exact computer enumerations indicate that the method can give accurate results for the entropy. The method developed here provides a solid first step toward a systematic development of a theory for the entropy and free energy landscape for complex tertiary folds for RNAs and proteins.
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