Institute of Bioinformatics and Medical Engineering , Jiangsu University of Technology , Changzhou , Jiangsu 213001 , China.
Department of Physics, Department of Biochemistry, and Informatics Institute , University of Missouri , Columbia , Missouri 65211 , United States.
J Phys Chem B. 2018 May 31;122(21):5327-5335. doi: 10.1021/acs.jpcb.7b10102. Epub 2018 Jan 8.
The current RNA structure prediction methods cannot keep up the pace of the rapidly increasing number of sequences and the emerging new functions of RNAs. Template-based RNA three-dimensional structure prediction methods are restricted by the limited number of known RNA structures, and traditional motif-based search for the templates does not always lead to successful results. Here we report a new template search and assembly algorithm, the hierarchical loop template-assembly method (VfoldLA). The method searches for templates for single strand loop/junctions instead of the whole motifs, which often renders no available templates, or short fragments (several nucleotides), which requires a long computational time to assemble and refine. The VfoldLA method has the advantage of accounting for local and nonlocal interloop interactions. Benchmark tests indicate that this new method can provide low-resolution predictions for RNA conformations at different levels of structural complexities. Furthermore, the VfoldLA-predicted conformations may also serve as reliable putative models for further structure prediction and refinements. VfoldLA is accessible at http://rna.physics.missouri.edu/vfoldLA .
目前的 RNA 结构预测方法无法跟上不断增加的序列数量和 RNA 新兴功能的步伐。基于模板的 RNA 三维结构预测方法受到已知 RNA 结构数量有限的限制，而传统的基于模体的模板搜索并不总是能取得成功。在这里，我们报告了一种新的模板搜索和组装算法，即层次环模板组装方法（VfoldLA）。该方法搜索单链环/连接的模板，而不是整个模体，这通常导致没有可用的模板，或者是短片段（几个核苷酸），这需要很长的计算时间来组装和细化。VfoldLA 方法的优点是可以考虑局部和非局部的环间相互作用。基准测试表明，这种新方法可以在不同结构复杂度水平上提供 RNA 构象的低分辨率预测。此外，VfoldLA 预测的构象也可以作为进一步结构预测和细化的可靠假定模型。VfoldLA 可在 http://rna.physics.missouri.edu/vfoldLA 获得。
