Le S Y, Chen J H, Maizel J V
Laboratory of Mathematical Biology, National Cancer Institute, NIH, Frederick, MD 21702.
Nucleic Acids Res. 1993 May 11;21(9):2173-8. doi: 10.1093/nar/21.9.2173.
In this paper we present a new method for predicting a set of RNA secondary structures that are thermodynamically favored in RNA folding simulations. This method uses a large number of 'simulated energy rules' (SER) generated by perturbing the free energy parameters derived experimentally within the range of the experimental errors. The structure with the lowest free energy is computed for each SER. Structural comparisons are used to avoid multiple generation of similar structures. Computed structures are evaluated using the energy distribution of the lowest free energy structures derived in the simulation. Predicted be graphically displayed with their occurring frequencies in the simulation by dot-plot representations. On average, about 90% of phylogenetic helixes in the known models of tRNA, Group I self-splicing intron, and Escherichia coli 16 S rRNA, were predicted using the method.
在本文中，我们提出了一种新方法，用于预测在RNA折叠模拟中热力学上有利的一组RNA二级结构。该方法使用大量通过在实验误差范围内扰动实验得出的自由能参数而生成的“模拟能量规则”（SER）。针对每个SER计算具有最低自由能的结构。通过结构比较来避免相似结构的多次生成。使用模拟中得出的最低自由能结构的能量分布来评估计算得到的结构。预测结果将通过点图表示法以其在模拟中的出现频率进行图形显示。平均而言，使用该方法可以预测出已知的tRNA模型、I类自我剪接内含子和大肠杆菌16S rRNA中约90%的系统发育螺旋。
