Morris Garrett M, Huey Ruth, Olson Arthur J
The Scripps Research Institute, La Jolla, California, USA.
Curr Protoc Bioinformatics. 2008 Dec;Chapter 8:Unit 8.14. doi: 10.1002/0471250953.bi0814s24.
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.
本单元介绍了如何使用AutoDock和图形用户界面AutoDockTools（ADT）来设置和分析配体-蛋白质对接计算。AutoDock评分函数是AMBER力场的一个子集，它使用联合原子模型来处理分子。本单元使用从蛋白质数据库（第1.9单元）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准备配体和受体，AutoGrid用于计算AutoDock所需的网格图。为AutoDock准备茚地那韦，添加极性氢和部分电荷，并定义对接过程中要探索的可旋转键。创建AutoGrid和AutoDock的输入文件，然后运行网格图计算，接着在AutoDock中进行对接计算。最后，本单元描述了一些使用AutoDockTools分析结果的方法。
