ArticleProceedings of the National Academy of Sciences of the United States of America2011
Clustering to identify RNA conformations constrained by secondary structure.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2011. 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.
- Predicting RNA Scaffolds with a Hybrid Method of Vfold3D and VfoldLA.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Topological constraints of RNA pseudoknotted and loop-kissing motifs: applications to three-dimensional structure prediction.Nucleic acids research · 2020Article
- Predicting 3D structure and stability of RNA pseudoknots in monovalent and divalent ion solutions.PLoS computational biology · 2018Article
- Nucleotide Dependent Switching in Rho GTPase: Conformational Heterogeneity and Competing Molecular Interactions.Scientific reports · 2017Article
- Structure Prediction: New Insights into Decrypting Long Noncoding RNAs.International journal of molecular sciences · 2016Review
- Predicting RNA 3D structure using a coarse-grain helix-centered model.RNA (New York, N.Y.) · 2015Article
- Noncanonical secondary structure stabilizes mitochondrial tRNA(Ser(UCN)) by reducing the entropic cost of tertiary folding.Journal of the American Chemical Society · 2015Article
- Efficient in silico exploration of RNA interhelical conformations using Euler angles and WExplore.Nucleic acids research · 2014Article
- Topological constraints are major determinants of tRNA tertiary structure and dynamics and provide basis for tertiary folding cooperativity.Nucleic acids research · 2014Article
- Graph-based sampling for approximating global helical topologies of RNA.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Hierarchy of RNA functional dynamics.Annual review of biochemistry · 2014Review
- Article
- The impact of a ligand binding on strand migration in the SAM-I riboswitch.PLoS computational biology · 2013Article
- De novo automated design of small RNA circuits for engineering synthetic riboregulation in living cells.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- Determining RNA three-dimensional structures using low-resolution data.Journal of structural biology · 2012Article
- Structure and mechanical properties of the ribosomal L1 stalk three-way junction.Nucleic acids research · 2012Article
- Article
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2 authors.
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Abstract
RNA often folds hierarchically, so that its sequence defines its secondary structure (helical base-paired regions connected by single-stranded junctions), which subsequently defines its tertiary fold. To preserve base-pairing and chain connectivity, the three-dimensional conformations that RNA can explore are strongly confined compared to when secondary structure constraints are not enforced. Using three examples, we studied how secondary structure confines and dictates an RNA's preferred conformations. We made use of Macromolecular Conformations by SYMbolic programming (MC-Sym) fragment assembly to generate RNA conformations constrained by secondary structure. Then, to understand the correlations between different helix placements and orientations, we robustly clustered all RNA conformations by employing unique methods to remove outliers and estimate the best number of conformational clusters. We observed that the preferred conformation (as judged by largest cluster size) for each type of RNA junction molecule tested is consistent with its biological function. Further, the improved quality of models in our pruned datasets facilitates subsequent discrimination using scoring functions based either on statistical analysis (knowledge based) or experimental data.
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