AutoDock4(Zn): an improved AutoDock force field for small-molecule docking to zinc metalloproteins.
AutoDock4(Zn): an improved AutoDock force field for small-molecule docking to zinc metalloproteins.
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AutoDock4(Zn)：改进的 AutoDock 力场，用于小分子与锌金属蛋白的对接。
DOI：
10.1021/ci500209e
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发表时间：
2014-08-25
影响因子：
5.6
通讯作者：
Olson AJ
中科院分区：
文献类型：
--
作者：
Santos-Martins D;Forli S;Ramos MJ;Olson AJ
锌存在于多种蛋白质中，在大多数生物体的代谢中很重要。锌金属酶是疾病如癌症、心脏病、细菌感染和阿尔茨海默病的治疗相关靶标。在大多数情况下，靶向这些酶的药物分子建立与锌离子配位的相互作用。因此，准确预测配体与锌的相互作用是针对含锌蛋白质的计算对接和虚拟筛选的重要方面。我们已经扩展了AutoDock力场，包括一个专门的潜力，描述锌配位体的相互作用。这个势描述了相互作用的能量和几何分量。新的力场名为AutoDock4Zn，在292个含锌晶体复合物的数据集上进行了校准。重新对接的实验表明，力场提供了显着的改善性能，在两个自由能的结合估计，以及在均方根偏差从晶体结构的姿态。新力场已在AutoDock中实现，无需修改源代码。
Zinc is present in a wide variety of proteins and is important in the metabolism of most organisms. Zinc metalloenzymes are therapeutically relevant targets in diseases such as cancer, heart disease, bacterial infection, and Alzheimer’s disease. In most cases a drug molecule targeting such enzymes establishes an interaction that coordinates with the zinc ion. Thus, accurate prediction of the interaction of ligands with zinc is an important aspect of computational docking and virtual screening against zinc containing proteins. We have extended the AutoDock force field to include a specialized potential describing the interactions of zinc-coordinating ligands. This potential describes both the energetic and geometric components of the interaction. The new force field, named AutoDock4Zn, was calibrated on a data set of 292 crystal complexes containing zinc. Redocking experiments show that the force field provides significant improvement in performance in both free energy of binding estimation as well as in root-mean-square deviation from the crystal structure pose. The new force field has been implemented in AutoDock without modification to the source code.
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影响因子：
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作者：
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通讯作者：
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