使用罗塞塔FARFAR服务器对小型非规范RNA基序进行建模。
Modeling Small Noncanonical RNA Motifs with the Rosetta FARFAR Server.
作者信息
Yesselman Joseph D, Das Rhiju
机构信息
Biochemistry Department, Stanford University, Stanford, CA, 94305, USA.
Physics Department, Stanford University, Stanford, CA, 94305, USA.
出版信息
Methods Mol Biol. 2016;1490:187-98. doi: 10.1007/978-1-4939-6433-8_12.
Noncanonical RNA motifs help define the vast complexity of RNA structure and function, and in many cases, these loops and junctions are on the order of only ten nucleotides in size. Unfortunately, despite their small size, there is no reliable method to determine the ensemble of lowest energy structures of junctions and loops at atomic accuracy. This chapter outlines straightforward protocols using a webserver for Rosetta Fragment Assembly of RNA with Full Atom Refinement (FARFAR) ( http://rosie.rosettacommons.org/rna_denovo/submit ) to model the 3D structure of small noncanonical RNA motifs for use in visualizing motifs and for further refinement or filtering with experimental data such as NMR chemical shifts.
非经典RNA基序有助于定义RNA结构和功能的巨大复杂性，而且在许多情况下，这些环和连接仅为大约十个核苷酸的大小。遗憾的是，尽管它们尺寸小，但没有可靠的方法能以原子精度确定环和连接的最低能量结构集合。本章概述了使用一个网络服务器进行RNA全原子细化的Rosetta片段组装（FARFAR）（http://rosie.rosettacommons.org/rna_denovo/submit ）的直接方案，以对小型非经典RNA基序的三维结构进行建模，用于可视化基序以及利用诸如NMR化学位移等实验数据进行进一步细化或筛选。
Zotero 插件