Jolley Elizabeth A, Lewis Michael, Znosko Brent M
Department of Chemistry, Saint Louis University, 3501 Laclede Avenue, Saint Louis, Missouri, 63103, United States.
Chem Phys Lett. 2015 Oct 16;639:157-60. doi: 10.1016/j.cplett.2015.09.005.
A computational model for predicting RNA nearest neighbor free energy rankings has been expanded to include the nonstandard nucleotide inosine. The model uses average fiber diffraction data and molecular dynamic simulations to generate input geometries for Quantum mechanic calculations. This resulted in calculated intrastrand stacking, interstrand stacking, and hydrogen bonding energies that were combined to give total binding energies. Total binding energies for RNA dimer duplexes containing inosine were ranked and compared to experimentally determined free energy ranks for RNA duplexes containing inosine. Statistical analysis showed significant agreement between the computationally determined ranks and the experimentally determined ranks.
一种用于预测RNA最近邻自由能排名的计算模型已得到扩展，将非标准核苷酸肌苷纳入其中。该模型使用平均纤维衍射数据和分子动力学模拟来生成用于量子力学计算的输入几何结构。这产生了计算得到的链内堆积、链间堆积和氢键能，这些能量被组合起来得到总结合能。对含有肌苷的RNA二聚体双链体的总结合能进行排名，并与含有肌苷的RNA双链体的实验测定自由能排名进行比较。统计分析表明，计算确定的排名与实验确定的排名之间存在显著一致性。
