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首页> 外文会议>Computational Intelligence in Bioinformatics and Computational Biology, 2009. CIBCB '09 >rnaDesign: Local search for RNA secondary structure design
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rnaDesign: Local search for RNA secondary structure design

机译：rnaDesign：本地搜索RNA二级结构设计

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摘要

The RNA secondary structure design (SSD) problem is a recently emerging research topic motivated by applications such as customized drug design and the self-assembly of RNA nano-objects. This paper presents a novel local search algorithm, rnaDesign for SSD solving. An evaluation of the algorithm performance in terms of sequence affinity and structure specificity is made through comparison with another algorithm, RNAinverse. Experiments were performed on RNA secondary structures including three biologically existing data sets and one random structure set. Empirical results show that rnaDesign outperforms RNAinverse in terms of structure designability; sequences designed by rnaDesign also exhibit better thermodynamic stability with relatively lower folding energy. Furthermore, we demonstrate through parameter tuning experiments that using a combination of heuristic search strategies leads to better design performance; there also exists a strong correlation between the heuristic values in use and solution quality.
机译：RNA二级结构设计（SSD）问题是由诸如定制药物设计和RNA纳米物体的自组装等应用推动的新兴研究主题。本文提出了一种新颖的本地搜索算法rnaDesign来解决SSD问题。通过与另一种算法RNAinverse进行比较，评估了算法在序列亲和力和结构特异性方面的性能。对RNA二级结构进行了实验，该二级结构包括三个生物学上存在的数据集和一个随机结构集。实验结果表明，在结构可设计性方面，rnaDesign优于RNAinverse。 rnaDesign设计的序列也表现出更好的热力学稳定性，折叠能量相对较低。此外，我们通过参数调整实验证明，结合使用启发式搜索策略可带来更好的设计性能；使用中的启发式值与解决方案质量之间也存在很强的相关性。

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