RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers
RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers
复制标题
DOI：
10.1261/rna.075341.120
复制
发表时间：
2020-08-01
期刊：
影响因子：
4.5
通讯作者：
Westhof, Eric
中科院分区：
文献类型：
--
作者：
Miao, Zhichao;Adamiak, Ryszard W.;Westhof, Eric
RNA- puzzles是一个致力于推进和改进RNA 3D结构预测的集体努力。在晶体学家的一致意见下，RNA的结构在晶体结构发表之前就由不同的研究小组进行了预测。我们现在报告了六种RNA序列的3D结构预测：四种核溶酶和两种核开关。描述和分析了比较模型和晶体结构的系统协议。在这六个谜题中，我们讨论了(i)自动化web服务器与人类专家之间的比较；（ii）同轴叠加预测；（iii）结构细节和配体结合的预测；（四）发展新的预测方法；（五）需要改进的地方。研究表明，正确预测共轴堆叠和三级接触对于预测RNA结构至关重要，而配体结合模式只能以低分辨率预测，同时预测具有准确配体结合的RNA结构仍然遥不可及。这些预测模型可为未来力场参数的发展和比较评估工具的改进提供参考。
RNA-Puzzles is a collective endeavor dedicated to the advancement and improvement of RNA 3D structure prediction. With agreement from crystallographers, the RNA structures are predicted by various groups before the publication of the crystal structures. We now report the prediction of 3D structures for six RNA sequences: four nucleolytic ribozymes and two riboswitches. Systematic protocols for comparing models and crystal structures are described and analyzed. In these six puzzles, we discuss (i) the comparison between the automated web servers and human experts; (ii) the prediction of coaxial stacking; (iii) the prediction of structural details and ligand binding; (iv) the development of novel prediction methods; and (v) the potential improvements to be made. We show that correct prediction of coaxial stacking and tertiary contacts is essential for the prediction of RNA architecture, while ligand binding modes can only be predicted with low resolution and simultaneous prediction of RNA structure with accurate ligand binding still remains out of reach. All the predicted models are available for the future development of force field parameters and the improvement of comparison and assessment tools.