2019
DOI: 10.1093/nar/gkz1108
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RNA-Puzzles toolkit: a computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools

Abstract: Significant improvements have been made in the efficiency and accuracy of RNA 3D structure prediction methods during the succeeding challenges of RNA-Puzzles, a community-wide effort on the assessment of blind prediction of RNA tertiary structures. The RNA-Puzzles contest has shown, among others, that the development and validation of computational methods for RNA fold prediction strongly depend on the benchmark datasets and the structure comparison algorithms. Yet, there has been no systematic benchmark set o… Show more

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Cited by 69 publications
(90 citation statements)
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References 72 publications
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“…Homology modeling using templates may well capture the main topology but the local structural details in the loops of P2 and P3 regions show a difference from the crystal structure. It is not easy to evaluate how significant those changes are, since they occur in loop regions allowing dynamical movements and often with high crystallographic temperature factors as discussed previously (Miao and Westhof 2017;Magnus et al 2020). The correct modeling of such local structure variability continues to be a major challenge for the modeling methods.…”
Section: Detailed Prediction Resultsmentioning
confidence: 99%
See 1 more Smart Citation
“…Homology modeling using templates may well capture the main topology but the local structural details in the loops of P2 and P3 regions show a difference from the crystal structure. It is not easy to evaluate how significant those changes are, since they occur in loop regions allowing dynamical movements and often with high crystallographic temperature factors as discussed previously (Miao and Westhof 2017;Magnus et al 2020). The correct modeling of such local structure variability continues to be a major challenge for the modeling methods.…”
Section: Detailed Prediction Resultsmentioning
confidence: 99%
“…All the prediction results are available at www.rnapuzzles .org. The structure manipulation tools and all the assessment metrics together (Magnus et al 2020) with the predicted data are now available in an open-source repository at https://github.com/RNA-Puzzles.…”
Section: Availabilitymentioning
confidence: 99%
“…The quality of a density map depends on the resolution of the structure as well as the thermodynamic mobility of the molecule. It is known that structural regions of high-temperature factors (B factors) may not have a clear electron density to infer the atomic coordinates (Magnus et al, 2020). Thus, computational modeling may optimize the crystal structures using structure knowledge learned from already solved structures (Terayama et al, 2018).…”
Section: Rna Structure Characterization Experimentsmentioning
confidence: 99%
“…(https://github.com/mmagnus/PyMOL4Spliceosome) (Magnus et al 2019). Figures and movies containing molecular structures were generated using Pymol (Schrödinger).…”
Section: Structural Alignments and Figure Creationmentioning
confidence: 99%