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目的:评估QM/MM方法和Surflex-Dock分子对接程序对DNA-配体复合物模拟的准确性。方法:从蛋白质数据库(Protein Data Bank)下载DNA-配体复合物的三维结构,利用计算机辅助药物设计的分子对接程序Surflex-Dock模拟出147个诱饵化合物(decoys)并计算其结合分数(binding score)。然后将得出的分数与从QM/MM计算的结合能力以Z-score和辨别力(DP)作比较。从而评估Surflex-Dock和QM/MM的准确性。结果:Surflex-Dock的DPi值比QM/MM高,显示Surflex-Dock的辨别力较低。结论:因QM/MM计算速度慢,本研究认为Surflex-Dock可用作快速虚拟筛选,而较准确的QM/MM则适合用于对拥有较高结合分数的化合物进行再评分(rescoring)。
OBJECTIVE: To evaluate the accuracy of the QM / MM method and the Surflex-Dock molecular docking program for modeling DNA-ligand complexes. METHODS: The three-dimensional structure of the DNA-ligand complex was downloaded from the Protein Data Bank and 147 decoys were simulated using the software-designed molecular docking program Surflex-Dock. The binding score ). The resulting score is then compared to the Z-score and discrimination (DP) for binding capacity calculated from QM / MM. To evaluate the accuracy of Surflex-Dock and QM / MM. Results: The DPi value of Surflex-Dock is higher than that of QM / MM, indicating that Surflex-Dock is less discriminating. CONCLUSIONS: Due to the slow QM / MM calculations, the study concluded that Surflex-Dock can be used as a rapid virtual screen, while the more accurate QM / MM is suitable for rescoring compounds with higher binding scores.