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学科主题: 生命有机化学 ; 计算机化学与化学信息学
题名: 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
作者: Xu Y(许永) ; Wang RX(王任小)
通讯作者: 王任小
刊名: Proteins
发表日期: 2006-01-01
卷: 64, 期:4, 页:1058-1068
收录类别: SCI
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
英文摘要: 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.
语种: 英语
相关网址: 查看原文
内容类型: 期刊论文
URI标识: http://ir.sioc.ac.cn/handle/331003/27633
Appears in Collections:上海有机化学研究所_期刊论文

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Recommended Citation:
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.
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