超级计算机对接:蛋白质-配体复合物低能最小值的研究

D. Kutov, A. Sulimov, V. Sulimov
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引用次数: 10

摘要

结果表明,用PM7量子化学半经验方法和COSMO隐式溶剂模型计算蛋白质-配体复合物的整体能量最小值可确定为:首先,利用真空条件下MMFF94力场计算蛋白质-配体能量时,通过对接程序找到了低能量最小值;其次,用PM7方法和COSMO隐式溶剂模型重新计算了所有这些极小值的能量。第三,在这些重新计算的能量中,确定了最小能量,并且各自的最小值为PM7方法和COSMO隐式溶剂模型计算能量时的全局能量最小值。确定了MMFF94在真空中发现的低能极小值的最佳谱宽,以进行最少量的量子化学重新计算。该方法可以利用量子化学方法在溶剂中进行对接,提高对接定位精度。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Supercomputer Docking: Investigation of Low Energy Minima of Protein-Ligand Complexes
It is shown that the global energy minimum of a protein-ligand complex, when the energy is calculated by the PM7 quantum-chemical semiempirical method with the COSMO implicit solvent model, can be determined as follows. First, the low energy minima are found by a docking program when the protein-ligand energy is calculated with the MMFF94 force field in vacuum. Second, energies of all these minima are recalculated with the PM7 method and the COSMO implicit solvent model. Third, among these recalculated energies the minimal energy is determined and the respective minimum is the global energy minimum when the energy is calculated with the PM7 method and the COSMO implicit solvent model. The optimal width of the spectrum of low energy minima found with MMFF94 in vacuum is determined to perform minimal quantity of quantum-chemical recalculations. The proposed approach allows to perform docking in solvent with the quantum-chemical method and to increase the docking positioning accuracy.
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