PREDICTION OF ALTERNATIVE RNA SECONDARY STRUCTURES BASED ON FLUCTUATING THERMODYNAMIC PARAMETERS
PREDICTION OF ALTERNATIVE RNA SECONDARY STRUCTURES BASED ON FLUCTUATING THERMODYNAMIC PARAMETERS
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DOI：
10.1093/nar/21.9.2173
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发表时间：
1993-05-11
影响因子：
14.9
通讯作者：
MAIZEL, JV
中科院分区：
文献类型：
--
作者：
LE, SY;CHEN, JH;MAIZEL, JV
在本文中，我们提出了一种新的方法来预测一组RNA的二级结构，这是在RNA折叠模拟中非常有利的。这种方法使用了大量的“模拟能量规则”（SER）通过扰动的自由能参数实验得出的实验误差范围内产生的。对于每个SER，计算具有最低自由能的结构。结构比较用于避免多代相似结构。计算的结构进行评估，使用模拟中得到的最低自由能结构的能量分布。预测的结构和所有可能出现的螺旋茎可以图形化地显示与它们的出现频率在模拟中通过点图表示。平均而言，约90%的系统发育螺旋在已知的模型的tRNA，组I自我剪接内含子，和大肠杆菌16 S rRNA，预测使用的方法。
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 structures and all possible occurring helical stems can 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.