Papanicolaou C, Gouy M, Ninio J
Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):31-44. doi: 10.1093/nar/12.1part1.31.
A new set of energy values to predict the secondary structures in RNA molecules has been derived through a multiple-step refinement procedure. It achieves more than 80% success in predicting the cloverleaf pattern in tRNA (200 sequences tested) and more than 60% success in predicting the consensus folding of 5S RNA (100 sequences). Improvements in our initial program for predicting secondary structures, based on the principle of the "incompatibility islets" made possible the work on 5S RNA. The program was speeded up by introducing a dynamic grouping of the islets into three disjoint blocks. The novel features in the energy model include i) an evaluation of the contribution of odd pairs according to their position within a segment ii) a penalty for internal loops related to their dissymmetry iii) a bonus for bulge loops when the two terminal paired bases at the junction point are both pyrimidines.
通过多步优化程序得出了一组新的能量值，用于预测RNA分子中的二级结构。在预测tRNA中的三叶草结构时（测试了200个序列），成功率超过80%；在预测5S RNA的共有折叠时（100个序列），成功率超过60%。基于“不相容岛”原理，我们最初的二级结构预测程序得到了改进，从而能够开展5S RNA的研究工作。通过将岛动态分组为三个不相交的块，程序运行速度得以加快。能量模型的新特性包括：i）根据奇数对在片段中的位置评估其贡献；ii）对与不对称性相关的内环进行惩罚；iii）当连接点处的两个末端配对碱基均为嘧啶时，对凸起环给予奖励。
