AMDock (Assisted Molecular Docking) is a user-friendly graphical tool to assist in the docking of protein-ligand complexes using Autodock Vina and AutoDock4, including the option of using the Autodock4Zn force field for metalloproteins. AMDock integrates several external programs (Open Babel, PDB2PQR, AutoLigand, ADT scripts) to accurately prepare the input structure files and to optimally define the search space, offering several alternatives and different degrees of user supervision. For visualization of molecular structures, AMDock uses PyMOL, starting it automatically with several predefined visualization schemes to aid in setting up the box defining the search space and to visualize and analyze the docking results. One particularly useful feature implemented in AMDock is the off-target docking procedure that allows to conduct ligand selectivity studies easily. In summary, AMDock’s functional versatility makes it a very useful tool to conduct different docking studies, especially for beginners. The program is available, either for Windows or Linux, at https://github.com/Valdes-Tresanco-MS . This article was reviewed by Alexander Krah and Thomas Gaillard.

中文翻译：

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AMDock：一个多功能的图形工具，用于帮助 Autodock Vina 和 Autodock4 进行分子对接。

AMDock（辅助分子对接）是一种用户友好的图形工具，可帮助使用 Autodock Vina 和 AutoDock4 对接蛋白质-配体复合物，包括使用 Autodock4Zn 力场检测金属蛋白的选项。AMDock 集成了多个外部程序（Open Babel、PDB2PQR、AutoLigand、ADT 脚本）来准确准备输入结构文件并优化定义搜索空间，提供多种替代方案和不同程度的用户监督。对于分子结构的可视化，AMDock 使用 PyMOL，自动启动多个预定义的可视化方案，以帮助设置定义搜索空间的框，并可视化和分析对接结果。AMDock 中实现的一项特别有用的功能是脱靶对接程序，可以轻松进行配体选择性研究。总而言之，AMDock 的多功能性使其成为进行不同对接研究的非常有用的工具，尤其是对于初学者而言。该程序可用于 Windows 或 Linux，位于 https://github.com/Valdes-Tresanco-MS 。本文由 Alexander Krah 和 Thomas Gaillard 审阅。