基于波动热力学参数预测RNA二级结构异构体
Prediction of alternative RNA secondary structures based on fluctuating thermodynamic parameters.
作者信息
Le S Y, Chen J H, Maizel J V
机构信息
Laboratory of Mathematical Biology, National Cancer Institute, NIH, Frederick, MD 21702.
出版信息
Nucleic Acids Res. 1993 May 11;21(9):2173-8. doi: 10.1093/nar/21.9.2173.
Abstract
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.
摘要
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。
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本文引用的文献
1
Secondary structure model for 23S ribosomal RNA.23S核糖体RNA的二级结构模型
Nucleic Acids Res. 1981 Nov 25;9(22):6167-89. doi: 10.1093/nar/9.22.6167.
2
An energy model that predicts the correct folding of both the tRNA and the 5S RNA molecules.一种能预测转运核糖核酸（tRNA）和5S核糖核酸（5S RNA）分子正确折叠的能量模型。
Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):31-44. doi: 10.1093/nar/12.1part1.31.
3
Computer-aided nucleic acid secondary structure modeling incorporating enzymatic digestion data.结合酶切数据的计算机辅助核酸二级结构建模
Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):347-66. doi: 10.1093/nar/12.1part1.347.
4
Secondary structure of the Tetrahymena ribosomal RNA intervening sequence: structural homology with fungal mitochondrial intervening sequences.嗜热四膜虫核糖体RNA间隔序列的二级结构：与真菌线粒体间隔序列的结构同源性。
Proc Natl Acad Sci U S A. 1983 Jul;80(13):3903-7. doi: 10.1073/pnas.80.13.3903.
5
An RNA folding rule.一条RNA折叠规则。
Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):323-34. doi: 10.1093/nar/12.1part1.323.
6
Secondary structure of 16S ribosomal RNA.16S核糖体RNA的二级结构
Science. 1981 Apr 24;212(4493):403-11. doi: 10.1126/science.6163215.
7
Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information.利用热力学和辅助信息对大型RNA序列进行最优计算机折叠
Nucleic Acids Res. 1981 Jan 10;9(1):133-48. doi: 10.1093/nar/9.1.133.
8
Fast algorithm for predicting the secondary structure of single-stranded RNA.预测单链RNA二级结构的快速算法
Proc Natl Acad Sci U S A. 1980 Nov;77(11):6309-13. doi: 10.1073/pnas.77.11.6309.
9
Free energy of imperfect nucleic acid helices. II. Small hairpin loops.不完全核酸螺旋的自由能。II. 小发夹环
J Mol Biol. 1973 Feb 5;73(4):497-511. doi: 10.1016/0022-2836(73)90096-x.
10
Improved estimation of secondary structure in ribonucleic acids.核糖核酸二级结构的改进估计。
Nat New Biol. 1973 Nov 14;246(150):40-1. doi: 10.1038/newbio246040a0.
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