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A computational analysis of the binding affinities of FKBP12 inhibitors using the MM-PB/SA method drug design
其他题名A computational analysis of the binding affinities of FKBP12 inhibitors using the MM-PB/SA method drug design
Xu Y(许永); Wang RX(王任小)
2006
发表期刊Proteins
ISSN0887-3585
卷号64期号:4页码:1058-1068
摘要The FK506-binding proteins have been targets of pharmaceutical interests over years. We have studied the binding of a set of 12 nonimmunosuppressive small-molecule inhibitors to FKBP12 through molecular dynamics simulations. Each complex was subjected to 1-ns MD simulation conducted in an explicit solvent environment under constant temperature and pressure. The binding free energy of each complex was then computed by the MMPB/SA method in the AMBER program. Our MMPB/SA computation produced a good correlation between the experimentally determined and the computed binding free energies with a correlation coefficient (R-2) of 0.93 and a standard deviation as low as 0.30 kcal/mol. The vibrational entropy term given by the normal mode analysis was found to be helpful for achieving this correlation. Moreover, an adjustment to one weight factor in the PB/SA model was essential to correct the absolute values of the final binding free energies to a reasonable range. A head-to-head comparison of our MM-PB/SA model with a previously reported Linear Response Approximation (LRA) model suggested that the MMPB/SA method is more robust in binding affinity prediction for this class of compounds.
学科领域生命有机化学 ; 计算机化学与化学信息学
部门归属中国科学院上海有机化学研究所生命有机国家重点实验室
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收录类别SCI
语种英语
文献类型期刊论文
条目标识符http://ir.sioc.ac.cn/handle/331003/27633
专题上海有机化学研究所
通讯作者Wang RX(王任小)
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GB/T 7714
Xu Y,Wang RX. A computational analysis of the binding affinities of FKBP12 inhibitors using the MM-PB/SA method drug design[J]. Proteins,2006,64(4):1058-1068.
APA 许永,&王任小.(2006).A computational analysis of the binding affinities of FKBP12 inhibitors using the MM-PB/SA method drug design.Proteins,64(4),1058-1068.
MLA 许永,et al."A computational analysis of the binding affinities of FKBP12 inhibitors using the MM-PB/SA method drug design".Proteins 64.4(2006):1058-1068.
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