Coarse Grained Models Reveal Essential Contributions of Topological Constraints to the Conformational Free Energy of RNA Bulges

@inproceedings{Mustoe2014CoarseGM,
  title={Coarse
Grained Models Reveal Essential Contributions
of Topological Constraints to the Conformational Free Energy of RNA
Bulges},
  author={Anthony M Mustoe and Hashim M Al-Hashimi and Charles L. Brooks},
  booktitle={The journal of physical chemistry. B},
  year={2014}
}
Recent studies have shown that simple stereochemical constraints encoded at the RNA secondary structure level significantly restrict the orientation of RNA helices across two-way junctions and yield physically reasonable distributions of RNA 3D conformations. Here we develop a new coarse-grain model, TOPRNA, that is optimized for exploring detailed aspects of these topological constraints in complex RNA systems. Unlike prior models, TOPRNA effectively treats RNAs as collections of semirigid… CONTINUE READING

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