The overall geometry improvement may be associated with increased model accuracy, especially on the level of correctly modeled base-pairs, but the systematic improvement of root mean square deviation to the reference structure should not be expected. QRNAS was able to improve MolProbity scores of NMR structures, as well as of computational models generated in the course of the RNA-Puzzles experiment. We demonstrate the ability of QRNAS to improve the quality of models generated with different methods. QRNAS is capable of handling RNA, DNA, chimeras, and hybrids thereof, and enables modeling of nucleic acids containing modified residues. We present QRNAS, a software tool for fine-grained refinement of nucleic acid structures, which is an extension of the AMBER simulation method with additional restraints. The goal of the refinement is not only to improve the local quality of the model but to bring it globally closer to the true structure. To obtain a high-quality model, the preliminary RNA structural model needs to be refined, taking into account atomic interactions. Computational models of RNA 3D structure often present various inaccuracies caused by simplifications used in structure prediction methods, such as template-based modeling or coarse-grained simulations.
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