使用Rappertk进行RNA取样和晶体学精修
RNA sampling and crystallographic refinement using Rappertk
摘要：
背景RNA结构数据的急剧增加使人们能够比十年前更好地识别其构象偏好。这创造了一个机会，使用离散的限制为基础的构象采样建模RNA和自动化的结晶细化。结果使用Richardson RNA骨架旋转异构体库和糖苷二面角的无偏分布实现整个RNA链、末端和环的全原子采样。Rappertk在不同空间约束下的RNA链的不同数据集上的采样行为是基准的。这里开发的迭代复合晶体学精修协议被证明优于仅CNS精修tRNA（Asp）结构的一部分。结论这项工作为RNA建模和晶体学的进一步工作开辟了令人兴奋的可能性。
英文摘要：
Background. Dramatic increases in RNA structural data have made it possible to recognize its conformational preferences much better than a decade ago. This has created an opportunity to use discrete restraint-based conformational sampling for modelling RNA and automating its crystallographic refinement. Results. All-atom sampling of entire RNA chains, termini and loops is achieved using the Richardson RNA backbone rotamer library and an unbiased distribution for glycosidic dihedral angle. Sampling behaviour of Rappertk on a diverse dataset of RNA chains under varying spatial restraints is benchmarked. The iterative composite crystallographic refinement protocol developed here is demonstrated to outperform CNS-only refinement on parts of tRNA(Asp) structure. Conclusion. This work opens exciting possibilities for further work in RNA modelling and crystallography.
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