RR3DD: an RNA global structure-based RNA three-dimensional structural classification database

The three-dimensional (3D) structure of RNA usually plays an important role in the recognition with RNA-binding protein. Along with the discovering of RNAs, several RNA databases are developed to study the functions of RNA based on sequence, secondary structure, local 3D structural motif and global structure. Based on RNA function and structure, different RNAs are classified and stored in SCOR and DARTS, respectively. The classification of RNA structures is useful in RNA structure prediction and function annotation. However, the SCOR and DARTS are not updated any more. In this study, we present an RNA classification database RR3DD based on RNA fold with the global 3D structural similarity. The RR3DD includes 13,601 RNA chains from PDB and mmCIF format structures which are classified into 780 RNA folds. The RNA chains from PDB and mmCIF format structures are aligned and clustered into 675 and 220 RNA folds, respectively. By analysing the RNA structure in RR3DD, we find that there are 11 clusters with more than 50 members. These clusters include rRNAs, riboswitches, tRNAs and so on. By mapping RR3DD into Rfam, we found that some RNAs without annotation by Rfam can be annotated through structural alignment. For example, we analysed tRNAs and found that tRNA were successfully grouped in RR3DD for which Rfam did not classify them into one family. Finally, we provide a web interface of RR3DD offering functions of browsing RR3DD, annotating RNA 3D structure and finding templates for RNA homology modelling.

RNA的三维（3D）结构通常在与RNA结合蛋白（RNA-binding protein）的识别过程中发挥关键作用。随着各类RNA被陆续发现，学界已开发出多款RNA数据库，基于序列、二级结构、局部三维结构基序（local 3D structural motif）以及全局结构来研究RNA的功能。根据RNA的功能与结构特征，不同RNA分别被分类并存储于SCOR和DARTS数据库中。RNA结构分类对于RNA结构预测与功能注释具有重要价值，但SCOR与DARTS数据库现已停止更新。本研究基于RNA折叠（RNA fold）与全局三维结构相似性，构建了一款RNA分类数据库RR3DD。RR3DD收录了来自PDB与mmCIF格式结构的13601条RNA链，并将其划分为780个RNA折叠类。其中，来自PDB格式结构的RNA链经结构比对与聚类后分为675个RNA折叠类，来自mmCIF格式结构的则分为220个。通过对RR3DD中的RNA结构进行分析，我们发现共有11个成员数超过50的RNA折叠类，这些类涵盖了核糖体RNA（rRNA）、核糖开关（riboswitch）、转运RNA（tRNA）等类型。通过将RR3DD与Rfam数据库进行映射比对，我们发现部分未被Rfam注释的RNA可通过结构比对完成功能注释。例如，我们针对转运RNA开展分析后发现，RR3DD成功将原本未被Rfam归为同一家族的转运RNA聚集为一类。最后，本研究为RR3DD搭建了Web交互界面，提供RR3DD数据库浏览、RNA三维结构注释以及RNA同源建模模板检索等功能。