Centre of New Technologies, University of Warsaw, Warsaw, Poland.
Institute of Computing Science, Poznan University of Technology, Poznan, Poland.
PLoS Comput Biol. 2024 Jun 20;20(6):e1011959. doi: 10.1371/journal.pcbi.1011959. eCollection 2024 Jun.
Unlike proteins, RNAs deposited in the Protein Data Bank do not contain topological knots. Recently, admittedly, the first trefoil knot and some lasso-type conformations have been found in experimental RNA structures, but these are still exceptional cases. Meanwhile, algorithms predicting 3D RNA models have happened to form knotted structures not so rarely. Interestingly, machine learning-based predictors seem to be more prone to generate knotted RNA folds than traditional methods. A similar situation is observed for the entanglements of structural elements. In this paper, we analyze all models submitted to the CASP15 competition in the 3D RNA structure prediction category. We show what types of topological knots and structure element entanglements appear in the submitted models and highlight what methods are behind the generation of such conformations. We also study the structural aspect of susceptibility to entanglement. We suggest that predictors take care of an evaluation of RNA models to avoid publishing structures with artifacts, such as unusual entanglements, that result from hallucinations of predictive algorithms.
与蛋白质不同，存储在蛋白质数据库中的 RNA 不包含拓扑结。最近，诚然，第一个三叶结和一些套索型构象已经在实验 RNA 结构中被发现，但这些仍然是例外情况。与此同时，预测 3D RNA 模型的算法碰巧形成结的结构并不罕见。有趣的是，基于机器学习的预测器似乎比传统方法更容易产生结 RNA 折叠。对于结构元素的缠结也观察到类似的情况。在本文中，我们分析了在 CASP15 竞赛的 3D RNA 结构预测类别中提交的所有模型。我们展示了在提交的模型中出现了哪些类型的拓扑结和结构元素缠结，并强调了生成这些构象的方法。我们还研究了易缠结的结构方面。我们建议预测器注意 RNA 模型的评估，以避免发布具有伪影的结构，例如由预测算法的幻觉导致的异常缠结。
