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首页> 外文期刊>IEEE/ACM transactions on computational biology and bioinformatics >Estimating Energy Parameters for RNA Secondary Structure Predictions Using Both Experimental and Computational Data
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Estimating Energy Parameters for RNA Secondary Structure Predictions Using Both Experimental and Computational Data

机译：使用实验数据和计算数据估算RNA二级结构预测的能量参数

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摘要

Computational RNA secondary structure prediction depends on a large number of nearest-neighbor free-energy parameters, including 10 parameters for Watson-Crick stacked base pairs that were estimated from experimental measurements of the free energies of 90 RNA duplexes. These experimental data are provided by time-consuming and cost-intensive experiments. In contrast, various modified nucleotides in RNAs, which would affect not only their structures but also functions, have been found, and rapid determination of energy parameters for a such modified nucleotides is needed. To reduce the high cost of determining energy parameters, we propose a novel method to estimate energy parameters from both experimental and computational data, where the computational data are provided by a recently developed molecular dynamics simulation protocol. We evaluate our method for Watson-Crick stacked base pairs, and show that parameters estimated from 10 experimental data items and 10 computational data items can predict RNA secondary structures with accuracy comparable to that using conventional parameters. The results indicate that the combination of experimental free-energy measurements and molecular dynamics simulations is capable of estimating the thermodynamic properties of RNA secondary structures at lower cost.
机译：计算RNA二级结构的预测取决于大量最近邻的自由能参数，包括10个Watson-Crick堆积碱基对的参数，这些参数是通过对90个RNA双链体的自由能进行实验测量得出的。这些实验数据由耗时且成本高昂的实验提供。相反，已经发现RNA中不仅会影响其结构而且还会影响功能的各种修饰的核苷酸，并且需要快速确定这种修饰的核苷酸的能量参数。为了减少确定能量参数的高成本，我们提出了一种从实验数据和计算数据中估算能量参数的新颖方法，其中，计算数据由最近开发的分子动力学模拟协议提供。我们评估了Watson-Crick堆叠碱基对的方法，并表明从10个实验数据项和10个计算数据项估计的参数可以预测RNA二级结构，其准确性与使用常规参数相当。结果表明，实验自由能测量和分子动力学模拟的结合能够以较低的成本估算RNA二级结构的热力学性质。

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