Dirks Robert M, Pierce Niles A
Department of Chemistry, California Institute of Technology, Pasadena, California 91125, USA.
J Comput Chem. 2003 Oct;24(13):1664-77. doi: 10.1002/jcc.10296.
Nucleic acid secondary structure models usually exclude pseudoknots due to the difficulty of treating these nonnested structures efficiently in structure prediction and partition function algorithms. Here, the standard secondary structure energy model is extended to include the most physically relevant pseudoknots. We describe an O(N(5)) dynamic programming algorithm, where N is the length of the strand, for computing the partition function and minimum energy structure over this class of secondary structures. Hence, it is possible to determine the probability of sampling the lowest energy structure, or any other structure of particular interest. This capability motivates the use of the partition function for the design of DNA or RNA molecules for bioengineering applications.
核酸二级结构模型通常不包括假结，因为在结构预测和配分函数算法中有效处理这些非嵌套结构存在困难。在此，标准二级结构能量模型被扩展以纳入最具物理相关性的假结。我们描述了一种O(N(5))动态规划算法（其中N是链的长度），用于计算此类二级结构的配分函数和最小能量结构。因此，有可能确定采样最低能量结构或任何其他特定感兴趣结构的概率。这种能力促使在生物工程应用中利用配分函数来设计DNA或RNA分子。
