Zuker M
Division of Biological Sciences, National Research Council of Canada, Ottawa, Ontario.
Science. 1989 Apr 7;244(4900):48-52. doi: 10.1126/science.2468181.
An algorithm and a computer program have been prepared for determining RNA secondary structures within any prescribed increment of the computed global minimum free energy. The mathematical problem of determining how well defined a minimum energy folding is can now be solved. All predicted base pairs that can participate in suboptimal structures may be displayed and analyzed graphically. Representative suboptimal foldings are generated by selecting these base pairs one at a time and computing the best foldings that contain them. A distance criterion that ensures that no two structures are "too close" is used to avoid multiple generation of similar structures. Thermodynamic parameters, including free-energy increments for single-base stacking at the ends of helices and for terminal mismatched pairs in interior and hairpin loops, are incorporated into the underlying folding model of the above algorithm.
已经准备了一种算法和一个计算机程序，用于在计算出的全局最小自由能的任何规定增量范围内确定RNA二级结构。现在可以解决确定最小能量折叠定义程度的数学问题。所有可能参与次优结构的预测碱基对都可以以图形方式显示和分析。通过一次选择一个碱基对并计算包含它们的最佳折叠来生成代表性的次优折叠。使用一种距离标准来确保没有两个结构“过于接近”，以避免多次生成相似结构。热力学参数，包括螺旋末端单碱基堆积以及内部环和发夹环中末端错配碱基对的自由能增量，被纳入上述算法的基础折叠模型中。
