Estimating energy parameters for RNA secondary structure predictions using both experimental and computational data
Estimating energy parameters for RNA secondary structure predictions using both experimental and computational data
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使用实验和计算数据估计 RNA 二级结构预测的能量参数
DOI：
10.1109/tcbb.2018.2813388
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发表时间：
2018
期刊：
影响因子：
--
通讯作者：
and Michiaki Hamada
中科院分区：
文献类型：
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作者：
Shimpei Nishida;Shun Sakuraba;Kiyoshi Asai;and Michiaki Hamada
计算RNA二级结构预测依赖于大量的最近邻自由能参数，包括10个参数沃森-克里克堆叠的碱基对，估计从实验测量的90 RNA双链体的自由能。这些实验数据是通过耗时且成本密集的实验提供的。与此相反，RNA中的各种修饰的核苷酸，这将不仅影响其结构，而且功能，已被发现，并需要快速测定这种修饰的核苷酸的能量参数。为了降低确定能量参数的高成本，我们提出了一种新的方法来估计能量参数的实验和计算数据，其中计算数据是由最近开发的分子动力学模拟协议。我们评估我们的方法沃森-克里克堆叠的碱基对，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二级结构的准确性与使用传统的参数。结果表明，结合实验自由能测量和分子动力学模拟是能够估计RNA二级结构的热力学性质，在较低的成本。
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.