MODENA: a multi-objective RNA inverse folding
MODENA: a multi-objective RNA inverse folding
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MODENA：多目标RNA反向折叠
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发表时间：
2010
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通讯作者：
A. Taneda
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作者：
A. Taneda
人工合成的RNA分子最近得到了研究，因为这种分子有可能产生各种新的功能分子。在设计人工RNA序列时，应考虑二级结构，因为非编码RNA的功能强烈依赖于它们的结构。RNA逆折叠是一种用于计算探索RNA序列折叠成用户给定目标结构的方法。在本研究中，我们开发了一种多目标遗传算法，MODENA（多目标设计的核酸），用于RNA逆折叠。MODENA探索目标函数空间中2个目标函数、一个结构稳定性评分和一个结构相似性评分的弱Pareto最优解的近似集。MODENA可以在一次运行中同时设计多个不同的RNA序列，其最低自由能范围从非常稳定的值到接近天然对应序列的较高值。我们用Rfam数据库中的29个目标结构对MODENA和之前的RNA反折叠程序进行了基准测试，我们发现MODENA可以成功设计23个RNA序列折叠成目标结构；该结果优于其他基准RNA反折叠程序。多目标遗传算法为功能性生物分子设计提供了一个有用的框架。MODENA的可执行文件可从http://rna.eit.hirosaki-u.ac.jp/modena/获取。
Artificially synthesized RNA molecules have recently come under study since such molecules have a potential for creating a variety of novel functional molecules. When designing artificial RNA sequences, secondary structure should be taken into account since functions of noncoding RNAs strongly depend on their structure. RNA inverse folding is a methodology for computationally exploring the RNA sequences folding into a user-given target structure. In the present study, we developed a multi-objective genetic algorithm, MODENA (Multi-Objective DEsign of Nucleic Acids), for RNA inverse folding. MODENA explores the approximate set of weak Pareto optimal solutions in the objective function space of 2 objective functions, a structure stability score and structure similarity score. MODENA can simultaneously design multiple different RNA sequences at 1 run, whose lowest free energies range from a very stable value to a higher value near those of natural counterparts. MODENA and previous RNA inverse folding programs were benchmarked with 29 target structures taken from the Rfam database, and we found that MODENA can successfully design 23 RNA sequences folding into the target structures; this result is better than those of the other benchmarked RNA inverse folding programs. The multi-objective genetic algorithm gives a useful framework for a functional biomolecular design. Executable files of MODENA can be obtained at http://rna.eit.hirosaki-u.ac.jp/modena/.