HIV蛋白酶与抑制剂的结合自由能计算  

Free Energy Calculation on HIV Protease And Inhibitor

作　　者：段莉莉[1] 张庆刚[1] 

机构地区：[1]山东师范大学物理与电子科学学院,济南250014

出　　处：《德州学院学报》2008年第4期41-44,共4页Journal of Dezhou University

基　　金：国家自然科学基金(10474060)

摘　　要：采用分子动力学模拟和MM-PBSA相结合方法计算了HIV蛋白酶和抑制剂的结合自由能.并且运用能量分解方法考察了蛋白酶主要残基与抑制剂之间的相互作用.在MM-PBSA中,体系的焓通过分子力学方法(MM)得到,极性部分对溶剂化自由能的贡献通过求解有限差分Poisson-Boltzmann(PB)方程得到,非极性部分对溶剂化自由能的贡献通过估算溶剂可接近表面积(SA)拟合得到.In this paper, the binding free energy between HIV protease and inhibitor is calculated by molecular dynamics simulation with MM-PBSA method. The interaction between HIV protease and inhibitor is evaluated by energy decomposition analysis. In MM-PBSA, the enthalpy of system is calculated from molecular mechanics, The polar salvation free energy of system in water is obtained using the Poison-Boltzmann continuum solvent model. The nonpolar contribution is estimated from the solvent-accessible surface area using the MSMS program.

关 键 词：分子动力学 MM—PBSA HIV蛋白酶 

分 类 号：O641.12[理学—物理化学]