Using AutoDock for ligand-receptor docking.
Using AutoDock for ligand-receptor docking.
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DOI：
10.1002/0471250953.bi0814s24
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发表时间：
2008-12-01
影响因子：
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通讯作者：
Olson, Arthur J
中科院分区：
文献类型：
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作者：
Morris, Garrett M;Huey, Ruth;Olson, Arthur J
本单元介绍如何使用AutoDock和图形用户界面AutoDockTools（ADT）设置和分析配体-蛋白质对接计算。AutoDock评分功能是AMBER力场的一个子集，使用联合原子模型处理分子。该单元使用了从蛋白质数据库（UNIT 1.9）中获取的与HIV-1蛋白酶结合的茚地那韦的X射线晶体结构，并展示了如何为AutoGrid制备配体和受体，AutoGrid计算AutoDock所需的网格图。茚地那韦是为AutoDock准备的，添加极性氢和部分电荷，并定义将在对接期间探索的可旋转键。将创建AutoGrid和AutoDock的输入文件，然后运行栅格映射计算，然后在AutoDock中运行对接计算。最后，本单元介绍了使用AutoDockTools分析结果的一些方法。
This unit describes how to set up and analyze ligand-protein docking calculations using AutoDock and the graphical user interface, AutoDockTools (ADT). The AutoDock scoring function is a subset of the AMBER force field that treats molecules using the United Atom model. The unit uses an X-ray crystal structure of Indinavir bound to HIV-1 protease taken from the Protein Data Bank (UNIT 1.9) and shows how to prepare the ligand and receptor for AutoGrid, which computes grid maps needed by AutoDock. Indinavir is prepared for AutoDock, adding the polar hydrogens, and partial charges, and defining the rotatable bonds that will be explored during the docking. The input files for AutoGrid and AutoDock are created, and then the grid map calculation run, followed by the docking calculation in AutoDock. Finally, this unit describes some of the ways the results can be analyzed using AutoDockTools.