Nussinov R, Jacobson A B
Proc Natl Acad Sci U S A. 1980 Nov;77(11):6309-13. doi: 10.1073/pnas.77.11.6309.
A computer method is presented for finding the most stable secondary structures in long single-stranded RNAs. It is 1-2 orders of magnitude faster than existing codes. The time required for its application increases as N3 for a chain N nucleotides long. As many as 1000 nucleotides can be searched in a single run. The approach is systematic and builds an optimal structure in a straightforward inductive procedure based on an exact mathematical algorithm. Two simple half-matrices are constructed and the best folded form is read directly from the second matrix by a simple back-tracking procedure. The program utilizes published values for base-pairing energies to compute one structure with the lowest free energy.
提出了一种用于寻找长单链RNA中最稳定二级结构的计算机方法。它比现有代码快1至2个数量级。对于长度为N个核苷酸的链，其应用所需时间随N³增加。单次运行可搜索多达1000个核苷酸。该方法是系统性的，基于精确的数学算法，通过直接的归纳过程构建最优结构。构建两个简单的半矩阵，通过简单的回溯过程直接从第二个矩阵中读取最佳折叠形式。该程序利用已发表的碱基配对能量值来计算具有最低自由能的一种结构。
