Ogata H, Akiyama Y, Kanehisa M
Institute for Chemical Research, Kyoto University, Japan.
Nucleic Acids Res. 1995 Feb 11;23(3):419-26. doi: 10.1093/nar/23.3.419.
A new modeling technique for arriving at the three dimensional (3-D) structure of an RNA stem-loop has been developed based on a conformational search by a genetic algorithm and the following refinement by energy minimization. The genetic algorithm simultaneously optimizes a population of conformations in the predefined conformational space and generates 3-D models of RNA. The fitness function to be optimized by the algorithm has been defined to reflect the satisfaction of known conformational constraints. In addition to a term for distance constraints, the fitness function contains a term to constrain each local conformation near to a prepared template conformation. The technique has been applied to the two loops of tRNA, the anticodon loop and the T-loop, and has found good models with small root mean square deviations from the crystal structure. Slightly different models have also been found for the anticodon loop. The analysis of a collection of alternative models obtained has revealed statistical features of local variations at each base position.
基于遗传算法的构象搜索及随后的能量最小化优化，已开发出一种用于确定RNA茎环三维（3-D）结构的新建模技术。遗传算法在预定义的构象空间中同时优化一组构象，并生成RNA的三维模型。该算法要优化的适应度函数已被定义为反映已知构象约束的满足情况。除了距离约束项外，适应度函数还包含一项，用于将每个局部构象约束在接近准备好的模板构象的状态。该技术已应用于tRNA的两个环，即反密码子环和T环，并找到了与晶体结构具有较小均方根偏差的良好模型。对于反密码子环也发现了略有不同的模型。对所获得的一组替代模型的分析揭示了每个碱基位置局部变异的统计特征。
