Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu 300, Taiwan, R.O.C.
Nucleic Acids Res. 2010 Jul;38(Web Server issue):W340-7. doi: 10.1093/nar/gkq483. Epub 2010 May 27.
iPARTS is an improved web server for aligning two RNA 3D structures based on a structural alphabet (SA)-based approach. In particular, we first derive a Ramachandran-like diagram of RNAs by plotting nucleotides on a 2D axis using their two pseudo-torsion angles eta and . Next, we apply the affinity propagation clustering algorithm to this eta- plot to obtain an SA of 23-nt conformations. We finally use this SA to transform RNA 3D structures into 1D sequences of SA letters and continue to utilize classical sequence alignment methods to compare these 1D SA-encoded sequences and determine their structural similarities. iPARTS takes as input two RNA 3D structures in the PDB format and outputs their global alignment (for determining overall structural similarity), semiglobal alignments (for detecting structural motifs or substructures), local alignments (for finding locally similar substructures) and normalized local structural alignments (for identifying more similar local substructures without non-similar internal fragments), with graphical display that allows the user to visually view, rotate and enlarge the superposition of aligned RNA 3D structures. iPARTS is now available online at http://bioalgorithm.life.nctu.edu.tw/iPARTS/.
iPARTS 是一个改进的网页服务器，用于基于结构字母表（SA）方法对齐两个 RNA 3D 结构。具体来说，我们首先通过使用两个伪扭转角 eta 和 将核苷酸绘制在 2D 轴上来绘制 RNA 的类似于 Ramachandran 的图谱。接下来，我们将亲和传播聚类算法应用于此 eta 图，以获得 23-nt 构象的 SA。最后，我们使用这个 SA 将 RNA 3D 结构转换为 SA 字母的 1D 序列，并继续使用经典的序列比对方法来比较这些 1D SA 编码序列，并确定它们的结构相似性。iPARTS 以 PDB 格式的两个 RNA 3D 结构作为输入，并输出它们的全局对齐（用于确定整体结构相似性）、半全局对齐（用于检测结构基序或子结构）、局部对齐（用于查找局部相似的子结构）和归一化局部结构对齐（用于识别没有非相似内部片段的更相似的局部子结构），并带有图形显示，允许用户直观地查看、旋转和放大对齐的 RNA 3D 结构的叠加。iPARTS 现在可以在 http://bioalgorithm.life.nctu.edu.tw/iPARTS/ 在线访问。
