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New metrics for comparing and assessing discrepancies between RNA 3D structures and models.

机译:用于比较和评估RNA 3D结构和模型之间差异的新指标。

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摘要

To benchmark progress made in RNA three-dimensional modeling and assess newly developed techniques, reliable and meaningful comparison metrics and associated tools are necessary. Generally, the average root-mean-square deviations (RMSDs) are quoted. However, RMSD can be misleading since errors are spread over the whole molecule and do not account for the specificity of RNA base interactions. Here, we introduce two new metrics that are particularly suitable to RNAs: the deformation index and deformation profile. The deformation index is calibrated by the interaction network fidelity, which considers base-base-stacking and base-base-pairing interactions within the target structure. The deformation profile highlights dissimilarities between structures at the nucleotide scale for both intradomain and interdomain interactions. Our results show that there is little correlation between RMSD and interaction network fidelity. The deformation profile is a tool that allows for rapid assessment of the origins of discrepancies.
机译:为了基准化RNA三维建模的进展并评估新开发的技术,需要可靠且有意义的比较指标和相关工具。通常,引用平均均方根偏差(RMSD)。但是,RMSD可能会产生误导,因为错误会散布在整个分子上,并且无法说明RNA碱基相互作用的特异性。在这里,我们介绍两个特别适用于RNA的新指标:变形指数和变形曲线。变形指数是通过相互作用网络的保真度来校准的,该网络考虑了目标结构内的碱基-碱基堆叠和碱基-碱基配对相互作用。对于域内和域间相互作用,形变轮廓突出了核苷酸尺度上结构之间的差异。我们的结果表明,RMSD与交互网络保真度之间几乎没有相关性。变形轮廓是一种工具,可以快速评估差异的来源。

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