Article
Coarse grained models reveal essential contributions of topological constraints to the conformational free energy of RNA bulges.
The journal of physical chemistry. B - 13 Mar 2014
Mustoe Anthony M, Al-Hashimi Hashim M, Brooks Charles L
Abstract excerpt
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....
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